Merge pull request #127 from smith-chem-wisc/stefan-branch

move stuff
smith-chem-wisc · Mar 15, 2017 · 1b479f6 · 1b479f6
2 parents 2c726ec + 4d0654b
commit 1b479f6
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Showing 143 changed files with 193 additions and 157 deletions.
diff --git a/Benchmark/Benchmark.csproj b/Benchmark/Benchmark.csproj
@@ -51,6 +51,9 @@
     <Prefer32Bit>true</Prefer32Bit>
   </PropertyGroup>
   <ItemGroup>
+    <Reference Include="MathNet.Numerics, Version=3.17.0.0, Culture=neutral, processorArchitecture=MSIL">
+      <HintPath>..\packages\MathNet.Numerics.3.17.0\lib\net40\MathNet.Numerics.dll</HintPath>
+    </Reference>
     <Reference Include="System" />
     <Reference Include="System.Core" />
     <Reference Include="System.Xml.Linq" />
@@ -59,13 +62,17 @@
     <Reference Include="System.Data" />
     <Reference Include="System.Net.Http" />
     <Reference Include="System.Xml" />
+    <Reference Include="Zlib.Portable, Version=1.11.0.0, Culture=neutral, processorArchitecture=MSIL">
+      <HintPath>..\packages\Zlib.Portable.1.11.0\lib\portable-net4+sl5+wp8+win8+wpa81+MonoTouch+MonoAndroid\Zlib.Portable.dll</HintPath>
+    </Reference>
   </ItemGroup>
   <ItemGroup>
     <Compile Include="Program.cs" />
     <Compile Include="Properties\AssemblyInfo.cs" />
   </ItemGroup>
   <ItemGroup>
     <None Include="App.config" />
+    <None Include="packages.config" />
     <None Include="yeast_160126.xml.gz">
       <CopyToOutputDirectory>Always</CopyToOutputDirectory>
     </None>
@@ -83,38 +90,22 @@
     </BootstrapperPackage>
   </ItemGroup>
   <ItemGroup>
-    <ProjectReference Include="..\mzLib\Chemistry\Chemistry.csproj">
+    <WCFMetadata Include="Service References\" />
+  </ItemGroup>
+  <ItemGroup>
+    <ProjectReference Include="..\Chemistry\Chemistry.csproj">
       <Project>{cbe368bb-fc84-458d-8099-87a63d17aa3b}</Project>
       <Name>Chemistry</Name>
     </ProjectReference>
-    <ProjectReference Include="..\mzLib\MassSpecFiles\MzML\MzML.csproj">
-      <Project>{012434FB-88A9-4DEC-B887-5F64C0B481D4}</Project>
-      <Name>MzML</Name>
-    </ProjectReference>
-    <ProjectReference Include="..\mzLib\MassSpecFiles\Thermo\Thermo.csproj">
-      <Project>{24DC85FF-E97B-4140-9614-77DD8FDDD32F}</Project>
-      <Name>Thermo</Name>
-    </ProjectReference>
-    <ProjectReference Include="..\mzLib\MassSpectrometry\MassSpectrometry.csproj">
-      <Project>{6FEBB7ED-0BE6-4493-817E-CEFD4CBE61DD}</Project>
-      <Name>MassSpectrometry</Name>
-    </ProjectReference>
-    <ProjectReference Include="..\mzLib\Proteomics\Proteomics.csproj">
+    <ProjectReference Include="..\Proteomics\Proteomics.csproj">
       <Project>{4ab6ba94-b70c-4570-9ea6-165746d5b8e8}</Project>
       <Name>Proteomics</Name>
     </ProjectReference>
-    <ProjectReference Include="..\mzLib\Spectra\Spectra.csproj">
-      <Project>{088e4fcb-d580-4bad-a811-a1796a7666d2}</Project>
-      <Name>Spectra</Name>
-    </ProjectReference>
-    <ProjectReference Include="..\mzLib\UsefulProteomicsDatabases\UsefulProteomicsDatabases.csproj">
+    <ProjectReference Include="..\UsefulProteomicsDatabases\UsefulProteomicsDatabases.csproj">
       <Project>{16f857b5-4942-4fa2-b198-bd4d14c1b2e4}</Project>
       <Name>UsefulProteomicsDatabases</Name>
     </ProjectReference>
   </ItemGroup>
-  <ItemGroup>
-    <WCFMetadata Include="Service References\" />
-  </ItemGroup>
   <Import Project="$(MSBuildToolsPath)\Microsoft.CSharp.targets" />
   <PropertyGroup>
     <PreBuildEvent>xcopy /y /d  "$(SolutionDir)x64\$(Configuration)\*.dll" "$(ProjectDir)$(OutDir)"</PreBuildEvent>

diff --git a/mzLib/MassSpecFiles/MzML/packages.config → Benchmark/packages.config b/mzLib/MassSpecFiles/MzML/packages.config → Benchmark/packages.config
diff --git a/mzLib/Chemistry/ChemicalFormula.cs → Chemistry/ChemicalFormula.cs b/mzLib/Chemistry/ChemicalFormula.cs → Chemistry/ChemicalFormula.cs
diff --git a/mzLib/Chemistry/Chemistry.csproj → Chemistry/Chemistry.csproj b/mzLib/Chemistry/Chemistry.csproj → Chemistry/Chemistry.csproj
@@ -37,6 +37,9 @@
     <SignAssembly>false</SignAssembly>
   </PropertyGroup>
   <ItemGroup>
+    <Reference Include="MathNet.Numerics, Version=3.17.0.0, Culture=neutral, processorArchitecture=MSIL">
+      <HintPath>..\packages\MathNet.Numerics.3.17.0\lib\net40\MathNet.Numerics.dll</HintPath>
+    </Reference>
     <Reference Include="System" />
     <Reference Include="System.Core" />
     <Reference Include="System.Xml.Linq" />
@@ -45,6 +48,9 @@
     <Reference Include="System.Data" />
     <Reference Include="System.Net.Http" />
     <Reference Include="System.Xml" />
+    <Reference Include="Zlib.Portable, Version=1.11.0.0, Culture=neutral, processorArchitecture=MSIL">
+      <HintPath>..\packages\Zlib.Portable.1.11.0\lib\portable-net4+sl5+wp8+win8+wpa81+MonoTouch+MonoAndroid\Zlib.Portable.dll</HintPath>
+    </Reference>
   </ItemGroup>
   <ItemGroup>
     <Compile Include="ChemicalFormula.cs" />
@@ -60,6 +66,9 @@
       <SonarQubeExclude>true</SonarQubeExclude>
     </Compile>
   </ItemGroup>
+  <ItemGroup>
+    <None Include="packages.config" />
+  </ItemGroup>
   <Import Project="$(MSBuildToolsPath)\Microsoft.CSharp.targets" />
   <!-- To modify your build process, add your task inside one of the targets below and uncomment it. 
        Other similar extension points exist, see Microsoft.Common.targets.

diff --git a/mzLib/Chemistry/Chemistry.nuspec → Chemistry/Chemistry.nuspec b/mzLib/Chemistry/Chemistry.nuspec → Chemistry/Chemistry.nuspec
diff --git a/mzLib/Chemistry/ClassExtensions.cs → Chemistry/ClassExtensions.cs b/mzLib/Chemistry/ClassExtensions.cs → Chemistry/ClassExtensions.cs
diff --git a/mzLib/Chemistry/Constants.cs → Chemistry/Constants.cs b/mzLib/Chemistry/Constants.cs → Chemistry/Constants.cs
diff --git a/mzLib/Chemistry/Element.cs → Chemistry/Element.cs b/mzLib/Chemistry/Element.cs → Chemistry/Element.cs
diff --git a/...emistry/Interfaces/IHasChemicalFormula.cs → Chemistry/Interfaces/IHasChemicalFormula.cs b/...emistry/Interfaces/IHasChemicalFormula.cs → Chemistry/Interfaces/IHasChemicalFormula.cs
diff --git a/mzLib/Chemistry/Interfaces/IHasMass.cs → Chemistry/Interfaces/IHasMass.cs b/mzLib/Chemistry/Interfaces/IHasMass.cs → Chemistry/Interfaces/IHasMass.cs
diff --git a/mzLib/Chemistry/Isotope.cs → Chemistry/Isotope.cs b/mzLib/Chemistry/Isotope.cs → Chemistry/Isotope.cs
diff --git a/mzLib/Chemistry/IsotopicDistribution.cs → Chemistry/IsotopicDistribution.cs b/mzLib/Chemistry/IsotopicDistribution.cs → Chemistry/IsotopicDistribution.cs
diff --git a/mzLib/Chemistry/PeriodicTable.cs → Chemistry/PeriodicTable.cs b/mzLib/Chemistry/PeriodicTable.cs → Chemistry/PeriodicTable.cs
diff --git a/mzLib/Chemistry/Properties/AssemblyInfo.cs → Chemistry/Properties/AssemblyInfo.cs b/mzLib/Chemistry/Properties/AssemblyInfo.cs → Chemistry/Properties/AssemblyInfo.cs
diff --git a/...UsefulProteomicsDatabases/packages.config → Chemistry/packages.config b/...UsefulProteomicsDatabases/packages.config → Chemistry/packages.config
diff --git a/ClassLibrary1/AssemblyInfo.cpp → ManagedThermoHelperLayer/AssemblyInfo.cpp b/ClassLibrary1/AssemblyInfo.cpp → ManagedThermoHelperLayer/AssemblyInfo.cpp
diff --git a/ClassLibrary1/ClassLibrary1.cpp → ManagedThermoHelperLayer/ClassLibrary1.cpp b/ClassLibrary1/ClassLibrary1.cpp → ManagedThermoHelperLayer/ClassLibrary1.cpp
diff --git a/ClassLibrary1/ClassLibrary1.h → ManagedThermoHelperLayer/ClassLibrary1.h b/ClassLibrary1/ClassLibrary1.h → ManagedThermoHelperLayer/ClassLibrary1.h
diff --git a/ClassLibrary1/ClassLibrary1.vcxproj → ...edThermoHelperLayer/ClassLibrary1.vcxproj b/ClassLibrary1/ClassLibrary1.vcxproj → ...edThermoHelperLayer/ClassLibrary1.vcxproj
@@ -99,9 +99,8 @@
     <Image Include="app.ico" />
   </ItemGroup>
   <ItemGroup>
-    <ProjectReference Include="..\Win32Project8\Win32Project8.vcxproj">
+    <ProjectReference Include="..\UnmanagedThermoHelperLayer\Win32Project8.vcxproj">
       <Project>{8913a108-5d93-4af7-b273-89a06e817611}</Project>
-      <CopyLocalSatelliteAssemblies>true</CopyLocalSatelliteAssemblies>
     </ProjectReference>
   </ItemGroup>
   <Import Project="$(VCTargetsPath)\Microsoft.Cpp.targets" />

diff --git a/ClassLibrary1/ClassLibrary1.vcxproj.filters → ...HelperLayer/ClassLibrary1.vcxproj.filters b/ClassLibrary1/ClassLibrary1.vcxproj.filters → ...HelperLayer/ClassLibrary1.vcxproj.filters
diff --git a/ClassLibrary1/Stdafx.cpp → ManagedThermoHelperLayer/Stdafx.cpp b/ClassLibrary1/Stdafx.cpp → ManagedThermoHelperLayer/Stdafx.cpp
diff --git a/ClassLibrary1/Stdafx.h → ManagedThermoHelperLayer/Stdafx.h b/ClassLibrary1/Stdafx.h → ManagedThermoHelperLayer/Stdafx.h
diff --git a/ClassLibrary1/Win32Project8.h → ManagedThermoHelperLayer/Win32Project8.h b/ClassLibrary1/Win32Project8.h → ManagedThermoHelperLayer/Win32Project8.h
diff --git a/ClassLibrary1/app.ico → ManagedThermoHelperLayer/app.ico b/ClassLibrary1/app.ico → ManagedThermoHelperLayer/app.ico
diff --git a/ClassLibrary1/app.rc → ManagedThermoHelperLayer/app.rc b/ClassLibrary1/app.rc → ManagedThermoHelperLayer/app.rc
diff --git a/ClassLibrary1/resource.h → ManagedThermoHelperLayer/resource.h b/ClassLibrary1/resource.h → ManagedThermoHelperLayer/resource.h
diff --git a/...Spectrometry/Chromatogram/Chromatogram.cs → ...Spectrometry/Chromatogram/Chromatogram.cs b/...Spectrometry/Chromatogram/Chromatogram.cs → ...Spectrometry/Chromatogram/Chromatogram.cs
diff --git a/...matogram/ChromatographicElutionProfile.cs → ...matogram/ChromatographicElutionProfile.cs b/...matogram/ChromatographicElutionProfile.cs → ...matogram/ChromatographicElutionProfile.cs
diff --git a/...metry/Chromatogram/ChromatographicPeak.cs → ...metry/Chromatogram/ChromatographicPeak.cs b/...metry/Chromatogram/ChromatographicPeak.cs → ...metry/Chromatogram/ChromatographicPeak.cs
diff --git a/.../MassSpectrometry/DataScan/IMsDataScan.cs → MassSpectrometry/DataScan/IMsDataScan.cs b/.../MassSpectrometry/DataScan/IMsDataScan.cs → MassSpectrometry/DataScan/IMsDataScan.cs
diff --git a/...etry/DataScan/IMsDataScanWithPrecursor.cs → ...etry/DataScan/IMsDataScanWithPrecursor.cs b/...etry/DataScan/IMsDataScanWithPrecursor.cs → ...etry/DataScan/IMsDataScanWithPrecursor.cs
diff --git a/...b/MassSpectrometry/DataScan/MsDataScan.cs → MassSpectrometry/DataScan/MsDataScan.cs b/...b/MassSpectrometry/DataScan/MsDataScan.cs → MassSpectrometry/DataScan/MsDataScan.cs
diff --git a/...metry/DataScan/MsDataScanWithPrecursor.cs → ...metry/DataScan/MsDataScanWithPrecursor.cs b/...metry/DataScan/MsDataScanWithPrecursor.cs → ...metry/DataScan/MsDataScanWithPrecursor.cs
diff --git a/...assSpectrometry/Enums/DissociationType.cs → MassSpectrometry/Enums/DissociationType.cs b/...assSpectrometry/Enums/DissociationType.cs → MassSpectrometry/Enums/DissociationType.cs
diff --git a/.../MassSpectrometry/Enums/MzAnalyzerType.cs → MassSpectrometry/Enums/MzAnalyzerType.cs b/.../MassSpectrometry/Enums/MzAnalyzerType.cs → MassSpectrometry/Enums/MzAnalyzerType.cs
diff --git a/mzLib/MassSpectrometry/Enums/Polarity.cs → MassSpectrometry/Enums/Polarity.cs b/mzLib/MassSpectrometry/Enums/Polarity.cs → MassSpectrometry/Enums/Polarity.cs
diff --git a/...b/MassSpectrometry/Enums/SmoothingType.cs → MassSpectrometry/Enums/SmoothingType.cs b/...b/MassSpectrometry/Enums/SmoothingType.cs → MassSpectrometry/Enums/SmoothingType.cs
diff --git a/mzLib/MassSpectrometry/IIdentifications.cs → MassSpectrometry/IIdentifications.cs b/mzLib/MassSpectrometry/IIdentifications.cs → MassSpectrometry/IIdentifications.cs
diff --git a/mzLib/MassSpectrometry/IMsDataFile.cs → MassSpectrometry/IMsDataFile.cs b/mzLib/MassSpectrometry/IMsDataFile.cs → MassSpectrometry/IMsDataFile.cs
diff --git a/mzLib/MassSpectrometry/IMsDynamicDataFile.cs → MassSpectrometry/IMsDynamicDataFile.cs b/mzLib/MassSpectrometry/IMsDynamicDataFile.cs → MassSpectrometry/IMsDynamicDataFile.cs
diff --git a/mzLib/MassSpectrometry/IMsStaticDataFile.cs → MassSpectrometry/IMsStaticDataFile.cs b/mzLib/MassSpectrometry/IMsStaticDataFile.cs → MassSpectrometry/IMsStaticDataFile.cs
diff --git a/.../MassSpectrometry/MassSpectrometry.csproj → MassSpectrometry/MassSpectrometry.csproj b/.../MassSpectrometry/MassSpectrometry.csproj → MassSpectrometry/MassSpectrometry.csproj
@@ -68,7 +68,7 @@
     <Compile Include="Enums\SmoothingType.cs" />
   </ItemGroup>
   <ItemGroup>
-    <ProjectReference Include="..\..\MzLibUtil\MzLibUtil.csproj">
+    <ProjectReference Include="..\MzLibUtil\MzLibUtil.csproj">
       <Project>{B208FF5F-5A33-490D-9DDB-7C76F5600FC4}</Project>
       <Name>MzLibUtil</Name>
     </ProjectReference>

diff --git a/mzLib/MassSpectrometry/MsDataFile.cs → MassSpectrometry/MsDataFile.cs b/mzLib/MassSpectrometry/MsDataFile.cs → MassSpectrometry/MsDataFile.cs
diff --git a/mzLib/MassSpectrometry/MzSpectra/IMzPeak.cs → MassSpectrometry/MzSpectra/IMzPeak.cs b/mzLib/MassSpectrometry/MzSpectra/IMzPeak.cs → MassSpectrometry/MzSpectra/IMzPeak.cs
diff --git a/...MassSpectrometry/MzSpectra/IMzSpectrum.cs → MassSpectrometry/MzSpectra/IMzSpectrum.cs b/...MassSpectrometry/MzSpectra/IMzSpectrum.cs → MassSpectrometry/MzSpectra/IMzSpectrum.cs
diff --git a/mzLib/MassSpectrometry/MzSpectra/MzPeak.cs → MassSpectrometry/MzSpectra/MzPeak.cs b/mzLib/MassSpectrometry/MzSpectra/MzPeak.cs → MassSpectrometry/MzSpectra/MzPeak.cs
diff --git a/.../MassSpectrometry/MzSpectra/MzSpectrum.cs → MassSpectrometry/MzSpectra/MzSpectrum.cs b/.../MassSpectrometry/MzSpectra/MzSpectrum.cs → MassSpectrometry/MzSpectra/MzSpectrum.cs
diff --git a/...ssSpectrometry/Properties/AssemblyInfo.cs → MassSpectrometry/Properties/AssemblyInfo.cs b/...ssSpectrometry/Properties/AssemblyInfo.cs → MassSpectrometry/Properties/AssemblyInfo.cs
diff --git a/MzLibUtil/MzLibUtil.csproj b/MzLibUtil/MzLibUtil.csproj
@@ -31,6 +31,9 @@
     <CodeAnalysisRuleSet>MinimumRecommendedRules.ruleset</CodeAnalysisRuleSet>
   </PropertyGroup>
   <ItemGroup>
+    <Reference Include="MathNet.Numerics, Version=3.17.0.0, Culture=neutral, processorArchitecture=MSIL">
+      <HintPath>..\packages\MathNet.Numerics.3.17.0\lib\net40\MathNet.Numerics.dll</HintPath>
+    </Reference>
     <Reference Include="System" />
     <Reference Include="System.Core" />
     <Reference Include="System.Xml.Linq" />
@@ -39,6 +42,9 @@
     <Reference Include="System.Data" />
     <Reference Include="System.Net.Http" />
     <Reference Include="System.Xml" />
+    <Reference Include="Zlib.Portable, Version=1.11.0.0, Culture=neutral, processorArchitecture=MSIL">
+      <HintPath>..\packages\Zlib.Portable.1.11.0\lib\portable-net4+sl5+wp8+win8+wpa81+MonoTouch+MonoAndroid\Zlib.Portable.dll</HintPath>
+    </Reference>
   </ItemGroup>
   <ItemGroup>
     <Compile Include="ClassExtensions.cs" />
@@ -50,6 +56,9 @@
     <Compile Include="Tolerance.cs" />
     <Compile Include="ToleranceUnit.cs" />
   </ItemGroup>
+  <ItemGroup>
+    <None Include="packages.config" />
+  </ItemGroup>
   <Import Project="$(MSBuildToolsPath)\Microsoft.CSharp.targets" />
   <!-- To modify your build process, add your task inside one of the targets below and uncomment it. 
        Other similar extension points exist, see Microsoft.Common.targets.

diff --git a/mzLib/Spectra/packages.config → MzLibUtil/packages.config b/mzLib/Spectra/packages.config → MzLibUtil/packages.config
@@ -1,4 +1,5 @@
 <?xml version="1.0" encoding="utf-8"?>
 <packages>
   <package id="MathNet.Numerics" version="3.17.0" targetFramework="net451" />
+  <package id="Zlib.Portable" version="1.11.0" targetFramework="net451" />
 </packages>
diff --git a/mzLib/MassSpecFiles/MzML/IMzmlScan.cs → MzML/IMzmlScan.cs b/mzLib/MassSpecFiles/MzML/IMzmlScan.cs → MzML/IMzmlScan.cs
diff --git a/mzLib/MassSpecFiles/MzML/MzML.csproj → MzML/MzML.csproj b/mzLib/MassSpecFiles/MzML/MzML.csproj → MzML/MzML.csproj
@@ -34,17 +34,15 @@
     <CodeAnalysisRuleSet>MinimumRecommendedRules.ruleset</CodeAnalysisRuleSet>
   </PropertyGroup>
   <ItemGroup>
-    <Reference Include="MathNet.Numerics, Version=3.17.0.0, Culture=neutral, processorArchitecture=MSIL">
-      <HintPath>..\..\..\packages\MathNet.Numerics.3.17.0\lib\net40\MathNet.Numerics.dll</HintPath>
-      <Private>True</Private>
+    <Reference Include="nunit.framework, Version=3.6.1.0, Culture=neutral, PublicKeyToken=2638cd05610744eb, processorArchitecture=MSIL">
+      <HintPath>..\packages\NUnit.3.6.1\lib\net45\nunit.framework.dll</HintPath>
     </Reference>
     <Reference Include="System" />
     <Reference Include="System.Core" />
     <Reference Include="System.Numerics" />
     <Reference Include="System.Xml" />
     <Reference Include="Zlib.Portable, Version=1.11.0.0, Culture=neutral, processorArchitecture=MSIL">
-      <HintPath>..\..\..\packages\Zlib.Portable.1.11.0\lib\portable-net4+sl5+wp8+win8+wpa81+MonoTouch+MonoAndroid\Zlib.Portable.dll</HintPath>
-      <Private>True</Private>
+      <HintPath>..\packages\Zlib.Portable.1.11.0\lib\portable-net4+sl5+wp8+win8+wpa81+MonoTouch+MonoAndroid\Zlib.Portable.dll</HintPath>
     </Reference>
   </ItemGroup>
   <ItemGroup>
@@ -64,15 +62,15 @@
     <None Include="packages.config" />
   </ItemGroup>
   <ItemGroup>
-    <ProjectReference Include="..\..\..\MzLibUtil\MzLibUtil.csproj">
+    <ProjectReference Include="..\MzLibUtil\MzLibUtil.csproj">
       <Project>{B208FF5F-5A33-490D-9DDB-7C76F5600FC4}</Project>
       <Name>MzLibUtil</Name>
     </ProjectReference>
-    <ProjectReference Include="..\..\MassSpectrometry\MassSpectrometry.csproj">
+    <ProjectReference Include="..\MassSpectrometry\MassSpectrometry.csproj">
       <Project>{6febb7ed-0be6-4493-817e-cefd4cbe61dd}</Project>
       <Name>MassSpectrometry</Name>
     </ProjectReference>
-    <ProjectReference Include="..\..\Spectra\Spectra.csproj">
+    <ProjectReference Include="..\Spectra\Spectra.csproj">
       <Project>{088e4fcb-d580-4bad-a811-a1796a7666d2}</Project>
       <Name>Spectra</Name>
     </ProjectReference>

diff --git a/mzLib/MassSpecFiles/MzML/Mzml.cs → MzML/Mzml.cs b/mzLib/MassSpecFiles/MzML/Mzml.cs → MzML/Mzml.cs
diff --git a/mzLib/MassSpecFiles/MzML/MzmlMethods.cs → MzML/MzmlMethods.cs b/mzLib/MassSpecFiles/MzML/MzmlMethods.cs → MzML/MzmlMethods.cs
diff --git a/mzLib/MassSpecFiles/MzML/MzmlPeak.cs → MzML/MzmlPeak.cs b/mzLib/MassSpecFiles/MzML/MzmlPeak.cs → MzML/MzmlPeak.cs
diff --git a/mzLib/MassSpecFiles/MzML/MzmlScan.cs → MzML/MzmlScan.cs b/mzLib/MassSpecFiles/MzML/MzmlScan.cs → MzML/MzmlScan.cs
diff --git a/...ssSpecFiles/MzML/MzmlScanWithPrecursor.cs → MzML/MzmlScanWithPrecursor.cs b/...ssSpecFiles/MzML/MzmlScanWithPrecursor.cs → MzML/MzmlScanWithPrecursor.cs
diff --git a/mzLib/MassSpecFiles/MzML/MzmlSpectrum.cs → MzML/MzmlSpectrum.cs b/mzLib/MassSpecFiles/MzML/MzmlSpectrum.cs → MzML/MzmlSpectrum.cs
diff --git a/...SpecFiles/MzML/Properties/AssemblyInfo.cs → MzML/Properties/AssemblyInfo.cs b/...SpecFiles/MzML/Properties/AssemblyInfo.cs → MzML/Properties/AssemblyInfo.cs
diff --git a/...b/MassSpecFiles/MzML/XSD/mzML1_1_1_idx.cs → MzML/XSD/mzML1_1_1_idx.cs b/...b/MassSpecFiles/MzML/XSD/mzML1_1_1_idx.cs → MzML/XSD/mzML1_1_1_idx.cs
diff --git a/.../MassSpecFiles/MzML/mzML1.1.0.designer.cs → MzML/mzML1.1.0.designer.cs b/.../MassSpecFiles/MzML/mzML1.1.0.designer.cs → MzML/mzML1.1.0.designer.cs
diff --git a/MzML/packages.config b/MzML/packages.config
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="utf-8"?>
+<packages>
+  <package id="NUnit" version="3.6.1" targetFramework="net451" />
+  <package id="Zlib.Portable" version="1.11.0" targetFramework="net451" />
+</packages>
diff --git a/mzLib/Proteomics/AminoAcidPolymer.cs → Proteomics/AminoAcidPolymer.cs b/mzLib/Proteomics/AminoAcidPolymer.cs → Proteomics/AminoAcidPolymer.cs
diff --git a/mzLib/Proteomics/ChemicalFormulaFragment.cs → Proteomics/ChemicalFormulaFragment.cs b/mzLib/Proteomics/ChemicalFormulaFragment.cs → Proteomics/ChemicalFormulaFragment.cs
diff --git a/...Proteomics/ChemicalFormulaModification.cs → Proteomics/ChemicalFormulaModification.cs b/...Proteomics/ChemicalFormulaModification.cs → Proteomics/ChemicalFormulaModification.cs
diff --git a/mzLib/Proteomics/ChemicalFormulaTerminus.cs → Proteomics/ChemicalFormulaTerminus.cs b/mzLib/Proteomics/ChemicalFormulaTerminus.cs → Proteomics/ChemicalFormulaTerminus.cs
diff --git a/mzLib/Proteomics/DatabaseReference.cs → Proteomics/DatabaseReference.cs b/mzLib/Proteomics/DatabaseReference.cs → Proteomics/DatabaseReference.cs
diff --git a/mzLib/Proteomics/DigestionPoint.cs → Proteomics/DigestionPoint.cs b/mzLib/Proteomics/DigestionPoint.cs → Proteomics/DigestionPoint.cs
diff --git a/mzLib/Proteomics/Fragment.cs → Proteomics/Fragment.cs b/mzLib/Proteomics/Fragment.cs → Proteomics/Fragment.cs
diff --git a/mzLib/Proteomics/FragmentTypes.cs → Proteomics/FragmentTypes.cs b/mzLib/Proteomics/FragmentTypes.cs → Proteomics/FragmentTypes.cs
diff --git a/mzLib/Proteomics/Interfaces/IProtease.cs → Proteomics/Interfaces/IProtease.cs b/mzLib/Proteomics/Interfaces/IProtease.cs → Proteomics/Interfaces/IProtease.cs
diff --git a/mzLib/Proteomics/Modification.cs → Proteomics/Modification.cs b/mzLib/Proteomics/Modification.cs → Proteomics/Modification.cs
diff --git a/mzLib/Proteomics/ModificationCollection.cs → Proteomics/ModificationCollection.cs b/mzLib/Proteomics/ModificationCollection.cs → Proteomics/ModificationCollection.cs
diff --git a/mzLib/Proteomics/ModificationMotif.cs → Proteomics/ModificationMotif.cs b/mzLib/Proteomics/ModificationMotif.cs → Proteomics/ModificationMotif.cs
diff --git a/mzLib/Proteomics/ModificationSites.cs → Proteomics/ModificationSites.cs b/mzLib/Proteomics/ModificationSites.cs → Proteomics/ModificationSites.cs
diff --git a/mzLib/Proteomics/ModificationWithLocation.cs → Proteomics/ModificationWithLocation.cs b/mzLib/Proteomics/ModificationWithLocation.cs → Proteomics/ModificationWithLocation.cs
diff --git a/mzLib/Proteomics/ModificationWithMass.cs → Proteomics/ModificationWithMass.cs b/mzLib/Proteomics/ModificationWithMass.cs → Proteomics/ModificationWithMass.cs
diff --git a/...b/Proteomics/ModificationWithMassAndCf.cs → Proteomics/ModificationWithMassAndCf.cs b/...b/Proteomics/ModificationWithMassAndCf.cs → Proteomics/ModificationWithMassAndCf.cs
diff --git a/mzLib/Proteomics/OldSchoolModification.cs → Proteomics/OldSchoolModification.cs b/mzLib/Proteomics/OldSchoolModification.cs → Proteomics/OldSchoolModification.cs
diff --git a/...lModificationWithMultiplePossibilities.cs → ...lModificationWithMultiplePossibilities.cs b/...lModificationWithMultiplePossibilities.cs → ...lModificationWithMultiplePossibilities.cs
diff --git a/mzLib/Proteomics/Peptide.cs → Proteomics/Peptide.cs b/mzLib/Proteomics/Peptide.cs → Proteomics/Peptide.cs
diff --git a/mzLib/Proteomics/Properties/AssemblyInfo.cs → Proteomics/Properties/AssemblyInfo.cs b/mzLib/Proteomics/Properties/AssemblyInfo.cs → Proteomics/Properties/AssemblyInfo.cs
diff --git a/mzLib/Proteomics/Protein.cs → Proteomics/Protein.cs b/mzLib/Proteomics/Protein.cs → Proteomics/Protein.cs
diff --git a/mzLib/Proteomics/ProteolysisProduct.cs → Proteomics/ProteolysisProduct.cs b/mzLib/Proteomics/ProteolysisProduct.cs → Proteomics/ProteolysisProduct.cs
diff --git a/mzLib/Proteomics/Proteomics.csproj → Proteomics/Proteomics.csproj b/mzLib/Proteomics/Proteomics.csproj → Proteomics/Proteomics.csproj
@@ -73,7 +73,7 @@
     <Compile Include="Terminus.cs" />
   </ItemGroup>
   <ItemGroup>
-    <ProjectReference Include="..\..\MzLibUtil\MzLibUtil.csproj">
+    <ProjectReference Include="..\MzLibUtil\MzLibUtil.csproj">
       <Project>{b208ff5f-5a33-490d-9ddb-7c76f5600fc4}</Project>
       <Name>MzLibUtil</Name>
     </ProjectReference>

diff --git a/mzLib/Proteomics/Proteomics.nuspec → Proteomics/Proteomics.nuspec b/mzLib/Proteomics/Proteomics.nuspec → Proteomics/Proteomics.nuspec
diff --git a/mzLib/Proteomics/Residue.cs → Proteomics/Residue.cs b/mzLib/Proteomics/Residue.cs → Proteomics/Residue.cs
diff --git a/mzLib/Proteomics/Terminus.cs → Proteomics/Terminus.cs b/mzLib/Proteomics/Terminus.cs → Proteomics/Terminus.cs
diff --git a/...eomics/Util/AminoAcidPolymerExtensions.cs → ...eomics/Util/AminoAcidPolymerExtensions.cs b/...eomics/Util/AminoAcidPolymerExtensions.cs → ...eomics/Util/AminoAcidPolymerExtensions.cs
diff --git a/mzLib/Spectra/IPeak.cs → Spectra/IPeak.cs b/mzLib/Spectra/IPeak.cs → Spectra/IPeak.cs
diff --git a/mzLib/Spectra/ISpectrum.cs → Spectra/ISpectrum.cs b/mzLib/Spectra/ISpectrum.cs → Spectra/ISpectrum.cs
diff --git a/mzLib/Spectra/Peak.cs → Spectra/Peak.cs b/mzLib/Spectra/Peak.cs → Spectra/Peak.cs
diff --git a/mzLib/Spectra/Properties/AssemblyInfo.cs → Spectra/Properties/AssemblyInfo.cs b/mzLib/Spectra/Properties/AssemblyInfo.cs → Spectra/Properties/AssemblyInfo.cs
diff --git a/mzLib/Spectra/Spectra.csproj → Spectra/Spectra.csproj b/mzLib/Spectra/Spectra.csproj → Spectra/Spectra.csproj
@@ -34,8 +34,10 @@
   </PropertyGroup>
   <ItemGroup>
     <Reference Include="MathNet.Numerics, Version=3.17.0.0, Culture=neutral, processorArchitecture=MSIL">
-      <HintPath>..\..\packages\MathNet.Numerics.3.17.0\lib\net40\MathNet.Numerics.dll</HintPath>
-      <Private>True</Private>
+      <HintPath>..\packages\MathNet.Numerics.3.17.0\lib\net40\MathNet.Numerics.dll</HintPath>
+    </Reference>
+    <Reference Include="nunit.framework, Version=3.6.1.0, Culture=neutral, PublicKeyToken=2638cd05610744eb, processorArchitecture=MSIL">
+      <HintPath>..\packages\NUnit.3.6.1\lib\net45\nunit.framework.dll</HintPath>
     </Reference>
     <Reference Include="System" />
     <Reference Include="System.Core" />
@@ -56,14 +58,14 @@
     </Compile>
   </ItemGroup>
   <ItemGroup>
-    <None Include="packages.config" />
-  </ItemGroup>
-  <ItemGroup>
-    <ProjectReference Include="..\..\MzLibUtil\MzLibUtil.csproj">
+    <ProjectReference Include="..\MzLibUtil\MzLibUtil.csproj">
       <Project>{B208FF5F-5A33-490D-9DDB-7C76F5600FC4}</Project>
       <Name>MzLibUtil</Name>
     </ProjectReference>
   </ItemGroup>
+  <ItemGroup>
+    <None Include="packages.config" />
+  </ItemGroup>
   <Import Project="$(MSBuildToolsPath)\Microsoft.CSharp.targets" />
   <!-- To modify your build process, add your task inside one of the targets below and uncomment it. 
        Other similar extension points exist, see Microsoft.Common.targets.

diff --git a/mzLib/Spectra/Spectrum.cs → Spectra/Spectrum.cs b/mzLib/Spectra/Spectrum.cs → Spectra/Spectrum.cs
diff --git a/mzLib/MassSpecFiles/Thermo/packages.config → Spectra/packages.config b/mzLib/MassSpecFiles/Thermo/packages.config → Spectra/packages.config
@@ -1,4 +1,5 @@
 <?xml version="1.0" encoding="utf-8"?>
 <packages>
   <package id="MathNet.Numerics" version="3.17.0" targetFramework="net451" />
+  <package id="NUnit" version="3.6.1" targetFramework="net451" />
 </packages>
diff --git a/Test/Test.csproj b/Test/Test.csproj
@@ -29,7 +29,6 @@
   <ItemGroup>
     <Reference Include="MathNet.Numerics, Version=3.17.0.0, Culture=neutral, processorArchitecture=MSIL">
       <HintPath>..\packages\MathNet.Numerics.3.17.0\lib\net40\MathNet.Numerics.dll</HintPath>
-      <Private>True</Private>
     </Reference>
     <Reference Include="nunit.framework, Version=3.6.1.0, Culture=neutral, PublicKeyToken=2638cd05610744eb, processorArchitecture=MSIL">
       <HintPath>..\packages\NUnit.3.6.1\lib\net45\nunit.framework.dll</HintPath>
@@ -43,6 +42,9 @@
     <Reference Include="System.Data" />
     <Reference Include="System.Net.Http" />
     <Reference Include="System.Xml" />
+    <Reference Include="Zlib.Portable, Version=1.11.0.0, Culture=neutral, processorArchitecture=MSIL">
+      <HintPath>..\packages\Zlib.Portable.1.11.0\lib\portable-net4+sl5+wp8+win8+wpa81+MonoTouch+MonoAndroid\Zlib.Portable.dll</HintPath>
+    </Reference>
   </ItemGroup>
   <ItemGroup>
     <Compile Include="FakeMsDataFile.cs" />
@@ -67,35 +69,35 @@
     <Compile Include="TestTolerance.cs" />
   </ItemGroup>
   <ItemGroup>
-    <ProjectReference Include="..\MzLibUtil\MzLibUtil.csproj">
-      <Project>{b208ff5f-5a33-490d-9ddb-7c76f5600fc4}</Project>
-      <Name>MzLibUtil</Name>
-    </ProjectReference>
-    <ProjectReference Include="..\mzLib\Chemistry\Chemistry.csproj">
-      <Project>{CBE368BB-FC84-458D-8099-87A63D17AA3B}</Project>
+    <ProjectReference Include="..\Chemistry\Chemistry.csproj">
+      <Project>{cbe368bb-fc84-458d-8099-87a63d17aa3b}</Project>
       <Name>Chemistry</Name>
     </ProjectReference>
-    <ProjectReference Include="..\mzLib\MassSpecFiles\mzIdentML\mzIdentML.csproj">
-      <Project>{63D869DF-55D8-4043-AD89-F90462403EBB}</Project>
+    <ProjectReference Include="..\MassSpectrometry\MassSpectrometry.csproj">
+      <Project>{6febb7ed-0be6-4493-817e-cefd4cbe61dd}</Project>
+      <Name>MassSpectrometry</Name>
+    </ProjectReference>
+    <ProjectReference Include="..\mzIdentML\mzIdentML.csproj">
+      <Project>{63d869df-55d8-4043-ad89-f90462403ebb}</Project>
       <Name>mzIdentML</Name>
     </ProjectReference>
-    <ProjectReference Include="..\mzLib\MassSpecFiles\MzML\MzML.csproj">
-      <Project>{012434FB-88A9-4DEC-B887-5F64C0B481D4}</Project>
-      <Name>MzML</Name>
+    <ProjectReference Include="..\MzLibUtil\MzLibUtil.csproj">
+      <Project>{b208ff5f-5a33-490d-9ddb-7c76f5600fc4}</Project>
+      <Name>MzLibUtil</Name>
     </ProjectReference>
-    <ProjectReference Include="..\mzLib\MassSpectrometry\MassSpectrometry.csproj">
-      <Project>{6FEBB7ED-0BE6-4493-817E-CEFD4CBE61DD}</Project>
-      <Name>MassSpectrometry</Name>
+    <ProjectReference Include="..\MzML\MzML.csproj">
+      <Project>{012434fb-88a9-4dec-b887-5f64c0b481d4}</Project>
+      <Name>MzML</Name>
     </ProjectReference>
-    <ProjectReference Include="..\mzLib\Proteomics\Proteomics.csproj">
-      <Project>{4AB6BA94-B70C-4570-9EA6-165746D5B8E8}</Project>
+    <ProjectReference Include="..\Proteomics\Proteomics.csproj">
+      <Project>{4ab6ba94-b70c-4570-9ea6-165746d5b8e8}</Project>
       <Name>Proteomics</Name>
     </ProjectReference>
-    <ProjectReference Include="..\mzLib\Spectra\Spectra.csproj">
+    <ProjectReference Include="..\Spectra\Spectra.csproj">
       <Project>{088E4FCB-D580-4BAD-A811-A1796A7666D2}</Project>
       <Name>Spectra</Name>
     </ProjectReference>
-    <ProjectReference Include="..\mzLib\UsefulProteomicsDatabases\UsefulProteomicsDatabases.csproj">
+    <ProjectReference Include="..\UsefulProteomicsDatabases\UsefulProteomicsDatabases.csproj">
       <Project>{16f857b5-4942-4fa2-b198-bd4d14c1b2e4}</Project>
       <Name>UsefulProteomicsDatabases</Name>
     </ProjectReference>

diff --git a/Test/packages.config b/Test/packages.config
@@ -3,4 +3,5 @@
   <package id="MathNet.Numerics" version="3.17.0" targetFramework="net451" />
   <package id="NUnit" version="3.6.1" targetFramework="net451" />
   <package id="NUnit3TestAdapter" version="3.7.0" targetFramework="net451" />
+  <package id="Zlib.Portable" version="1.11.0" targetFramework="net451" />
 </packages>
diff --git a/TestThermo/TestThermo.csproj b/TestThermo/TestThermo.csproj
@@ -33,6 +33,9 @@
     <CodeAnalysisRuleSet>MinimumRecommendedRules.ruleset</CodeAnalysisRuleSet>
   </PropertyGroup>
   <ItemGroup>
+    <Reference Include="MathNet.Numerics, Version=3.17.0.0, Culture=neutral, processorArchitecture=MSIL">
+      <HintPath>..\packages\MathNet.Numerics.3.17.0\lib\net40\MathNet.Numerics.dll</HintPath>
+    </Reference>
     <Reference Include="nunit.framework, Version=3.6.1.0, Culture=neutral, PublicKeyToken=2638cd05610744eb, processorArchitecture=MSIL">
       <HintPath>..\packages\NUnit.3.6.1\lib\net45\nunit.framework.dll</HintPath>
     </Reference>
@@ -44,6 +47,9 @@
     <Reference Include="System.Data" />
     <Reference Include="System.Net.Http" />
     <Reference Include="System.Xml" />
+    <Reference Include="Zlib.Portable, Version=1.11.0.0, Culture=neutral, processorArchitecture=MSIL">
+      <HintPath>..\packages\Zlib.Portable.1.11.0\lib\portable-net4+sl5+wp8+win8+wpa81+MonoTouch+MonoAndroid\Zlib.Portable.dll</HintPath>
+    </Reference>
   </ItemGroup>
   <ItemGroup>
     <Compile Include="TestThermo.cs" />
@@ -56,26 +62,26 @@
     </None>
   </ItemGroup>
   <ItemGroup>
+    <ProjectReference Include="..\MassSpectrometry\MassSpectrometry.csproj">
+      <Project>{6febb7ed-0be6-4493-817e-cefd4cbe61dd}</Project>
+      <Name>MassSpectrometry</Name>
+    </ProjectReference>
     <ProjectReference Include="..\MzLibUtil\MzLibUtil.csproj">
       <Project>{B208FF5F-5A33-490D-9DDB-7C76F5600FC4}</Project>
       <Name>MzLibUtil</Name>
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-    <ProjectReference Include="..\mzLib\MassSpecFiles\MzML\MzML.csproj">
-      <Project>{012434FB-88A9-4DEC-B887-5F64C0B481D4}</Project>
+    <ProjectReference Include="..\MzML\MzML.csproj">
+      <Project>{012434fb-88a9-4dec-b887-5f64c0b481d4}</Project>
       <Name>MzML</Name>
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-    <ProjectReference Include="..\mzLib\MassSpecFiles\Thermo\Thermo.csproj">
-      <Project>{24DC85FF-E97B-4140-9614-77DD8FDDD32F}</Project>
-      <Name>Thermo</Name>
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-    <ProjectReference Include="..\mzLib\MassSpectrometry\MassSpectrometry.csproj">
-      <Project>{6febb7ed-0be6-4493-817e-cefd4cbe61dd}</Project>
-      <Name>MassSpectrometry</Name>
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-    <ProjectReference Include="..\mzLib\Spectra\Spectra.csproj">
-      <Project>{088e4fcb-d580-4bad-a811-a1796a7666d2}</Project>
+    <ProjectReference Include="..\Spectra\Spectra.csproj">
+      <Project>{088E4FCB-D580-4BAD-A811-A1796A7666D2}</Project>
       <Name>Spectra</Name>
     </ProjectReference>
+    <ProjectReference Include="..\Thermo\Thermo.csproj">
+      <Project>{24dc85ff-e97b-4140-9614-77dd8fddd32f}</Project>
+      <Name>Thermo</Name>
+    </ProjectReference>
   </ItemGroup>
   <ItemGroup>
     <Service Include="{82A7F48D-3B50-4B1E-B82E-3ADA8210C358}" />