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stefanks
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Merge pull request #258 from smith-chem-wisc/StefanBranch
tmt
2 parents 0388fc7 + fe139a2 commit 09fd209

12 files changed

+157
-124
lines changed

‎CMD/CMD.csproj

+28-22
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@@ -37,37 +37,37 @@
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<TreatWarningsAsErrors>true</TreatWarningsAsErrors>
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</PropertyGroup>
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<ItemGroup>
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<Reference Include="Chemistry, Version=1.0.129.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.129\lib\Chemistry.dll</HintPath>
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<Reference Include="Chemistry, Version=1.0.131.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.131\lib\Chemistry.dll</HintPath>
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</Reference>
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<Reference Include="ManagedThermoHelperLayer, Version=1.0.129.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.129\lib\ManagedThermoHelperLayer.dll</HintPath>
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<Reference Include="ManagedThermoHelperLayer, Version=1.0.131.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.131\lib\ManagedThermoHelperLayer.dll</HintPath>
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</Reference>
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<Reference Include="MassSpectrometry, Version=1.0.129.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.129\lib\MassSpectrometry.dll</HintPath>
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<Reference Include="MassSpectrometry, Version=1.0.131.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.131\lib\MassSpectrometry.dll</HintPath>
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</Reference>
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<Reference Include="MathNet.Numerics, Version=3.17.0.0, Culture=neutral, processorArchitecture=MSIL">
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<HintPath>..\packages\MathNet.Numerics.3.17.0\lib\net40\MathNet.Numerics.dll</HintPath>
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<Private>True</Private>
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</Reference>
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<Reference Include="mzIdentML, Version=1.0.129.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.129\lib\mzIdentML.dll</HintPath>
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<Reference Include="mzIdentML, Version=1.0.131.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.131\lib\mzIdentML.dll</HintPath>
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</Reference>
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<Reference Include="MzLibUtil, Version=1.0.129.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.129\lib\MzLibUtil.dll</HintPath>
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<Reference Include="MzLibUtil, Version=1.0.131.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.131\lib\MzLibUtil.dll</HintPath>
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</Reference>
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<Reference Include="MzML, Version=1.0.129.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.129\lib\MzML.dll</HintPath>
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<Reference Include="MzML, Version=1.0.131.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.131\lib\MzML.dll</HintPath>
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</Reference>
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<Reference Include="NetSerializer, Version=4.1.0.0, Culture=neutral, processorArchitecture=MSIL">
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<HintPath>..\packages\NetSerializer.4.1.0\lib\net45\NetSerializer.dll</HintPath>
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<Private>True</Private>
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</Reference>
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<Reference Include="Proteomics, Version=1.0.129.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.129\lib\Proteomics.dll</HintPath>
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<Reference Include="Proteomics, Version=1.0.131.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.131\lib\Proteomics.dll</HintPath>
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</Reference>
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<Reference Include="Spectra, Version=1.0.129.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.129\lib\Spectra.dll</HintPath>
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<Reference Include="Spectra, Version=1.0.131.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.131\lib\Spectra.dll</HintPath>
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</Reference>
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<Reference Include="System" />
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<Reference Include="System.Core" />
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<Reference Include="System.Data" />
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<Reference Include="System.Net.Http" />
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<Reference Include="System.Xml" />
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<Reference Include="Thermo, Version=1.0.129.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.129\lib\Thermo.dll</HintPath>
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<Reference Include="Thermo, Version=1.0.131.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.131\lib\Thermo.dll</HintPath>
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</Reference>
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<Reference Include="UsefulProteomicsDatabases, Version=1.0.129.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.129\lib\UsefulProteomicsDatabases.dll</HintPath>
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<Reference Include="UsefulProteomicsDatabases, Version=1.0.131.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.131\lib\UsefulProteomicsDatabases.dll</HintPath>
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</Reference>
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<Reference Include="Zlib.Portable, Version=1.11.0.0, Culture=neutral, processorArchitecture=MSIL">
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<HintPath>..\packages\Zlib.Portable.1.11.0\lib\portable-net4+sl5+wp8+win8+wpa81+MonoTouch+MonoAndroid\Zlib.Portable.dll</HintPath>
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</ProjectReference>
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</ItemGroup>
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<Import Project="$(MSBuildToolsPath)\Microsoft.CSharp.targets" />
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<Import Project="..\packages\mzLib.1.0.129\build\mzLib.targets" Condition="Exists('..\packages\mzLib.1.0.129\build\mzLib.targets')" />
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<Import Project="..\packages\mzLib.1.0.131\build\mzLib.targets" Condition="Exists('..\packages\mzLib.1.0.131\build\mzLib.targets')" />
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<Target Name="EnsureNuGetPackageBuildImports" BeforeTargets="PrepareForBuild">
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<PropertyGroup>
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<ErrorText>This project references NuGet package(s) that are missing on this computer. Use NuGet Package Restore to download them. For more information, see http://go.microsoft.com/fwlink/?LinkID=322105. The missing file is {0}.</ErrorText>
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</PropertyGroup>
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<Error Condition="!Exists('..\packages\mzLib.1.0.131\build\mzLib.targets')" Text="$([System.String]::Format('$(ErrorText)', '..\packages\mzLib.1.0.131\build\mzLib.targets'))" />
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</Target>
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<!-- To modify your build process, add your task inside one of the targets below and uncomment it.
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Other similar extension points exist, see Microsoft.Common.targets.
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<Target Name="BeforeBuild">
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</Target>
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<Target Name="AfterBuild">
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</Target>
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-->
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</Project>
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</Project>

‎CMD/packages.config

+1-1
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@@ -1,7 +1,7 @@
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<?xml version="1.0" encoding="utf-8"?>
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<packages>
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<package id="MathNet.Numerics" version="3.17.0" targetFramework="net451" />
4-
<package id="mzLib" version="1.0.129" targetFramework="net451" />
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<package id="mzLib" version="1.0.131" targetFramework="net451" />
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<package id="NetSerializer" version="4.1.0" targetFramework="net451" />
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<package id="Zlib.Portable" version="1.11.0" targetFramework="net451" />
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</packages>

‎EngineLayer/EngineLayer.csproj

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<TreatWarningsAsErrors>true</TreatWarningsAsErrors>
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</PropertyGroup>
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<ItemGroup>
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<Reference Include="Chemistry, Version=1.0.129.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.129\lib\Chemistry.dll</HintPath>
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<Reference Include="Chemistry, Version=1.0.131.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.131\lib\Chemistry.dll</HintPath>
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</Reference>
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<Reference Include="ManagedThermoHelperLayer, Version=1.0.129.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.129\lib\ManagedThermoHelperLayer.dll</HintPath>
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<Reference Include="ManagedThermoHelperLayer, Version=1.0.131.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.131\lib\ManagedThermoHelperLayer.dll</HintPath>
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</Reference>
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<Reference Include="MassSpectrometry, Version=1.0.129.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.129\lib\MassSpectrometry.dll</HintPath>
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<Reference Include="MassSpectrometry, Version=1.0.131.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.131\lib\MassSpectrometry.dll</HintPath>
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</Reference>
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<Reference Include="MathNet.Numerics, Version=3.17.0.0, Culture=neutral, processorArchitecture=MSIL">
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<HintPath>..\packages\MathNet.Numerics.3.17.0\lib\net40\MathNet.Numerics.dll</HintPath>
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<Private>True</Private>
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</Reference>
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<Reference Include="mzIdentML, Version=1.0.129.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.129\lib\mzIdentML.dll</HintPath>
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<Reference Include="mzIdentML, Version=1.0.131.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.131\lib\mzIdentML.dll</HintPath>
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</Reference>
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<Reference Include="MzLibUtil, Version=1.0.129.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.129\lib\MzLibUtil.dll</HintPath>
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<Reference Include="MzLibUtil, Version=1.0.131.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.131\lib\MzLibUtil.dll</HintPath>
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</Reference>
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<Reference Include="MzML, Version=1.0.129.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.129\lib\MzML.dll</HintPath>
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<Reference Include="MzML, Version=1.0.131.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.131\lib\MzML.dll</HintPath>
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</Reference>
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<Reference Include="Proteomics, Version=1.0.129.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.129\lib\Proteomics.dll</HintPath>
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<Reference Include="Proteomics, Version=1.0.131.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.131\lib\Proteomics.dll</HintPath>
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</Reference>
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<Reference Include="Spectra, Version=1.0.129.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.129\lib\Spectra.dll</HintPath>
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<Reference Include="Spectra, Version=1.0.131.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.131\lib\Spectra.dll</HintPath>
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</Reference>
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<Reference Include="System" />
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<Reference Include="System.Core" />
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<Reference Include="System.Data" />
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<Reference Include="System.Net.Http" />
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<Reference Include="System.Xml" />
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<Reference Include="Thermo, Version=1.0.129.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.129\lib\Thermo.dll</HintPath>
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<Reference Include="Thermo, Version=1.0.131.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.131\lib\Thermo.dll</HintPath>
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</Reference>
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<Reference Include="UsefulProteomicsDatabases, Version=1.0.129.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.129\lib\UsefulProteomicsDatabases.dll</HintPath>
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<Reference Include="UsefulProteomicsDatabases, Version=1.0.131.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.131\lib\UsefulProteomicsDatabases.dll</HintPath>
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</Reference>
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<Reference Include="Zlib.Portable, Version=1.11.0.0, Culture=neutral, processorArchitecture=MSIL">
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<HintPath>..\packages\Zlib.Portable.1.11.0\lib\portable-net4+sl5+wp8+win8+wpa81+MonoTouch+MonoAndroid\Zlib.Portable.dll</HintPath>
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</Content>
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</ItemGroup>
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<Import Project="$(MSBuildToolsPath)\Microsoft.CSharp.targets" />
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<Import Project="..\packages\mzLib.1.0.129\build\mzLib.targets" Condition="Exists('..\packages\mzLib.1.0.129\build\mzLib.targets')" />
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<Import Project="..\packages\mzLib.1.0.131\build\mzLib.targets" Condition="Exists('..\packages\mzLib.1.0.131\build\mzLib.targets')" />
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<Target Name="EnsureNuGetPackageBuildImports" BeforeTargets="PrepareForBuild">
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<PropertyGroup>
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<ErrorText>This project references NuGet package(s) that are missing on this computer. Use NuGet Package Restore to download them. For more information, see http://go.microsoft.com/fwlink/?LinkID=322105. The missing file is {0}.</ErrorText>
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</PropertyGroup>
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<Error Condition="!Exists('..\packages\mzLib.1.0.131\build\mzLib.targets')" Text="$([System.String]::Format('$(ErrorText)', '..\packages\mzLib.1.0.131\build\mzLib.targets'))" />
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</Target>
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<!-- To modify your build process, add your task inside one of the targets below and uncomment it.
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Other similar extension points exist, see Microsoft.Common.targets.
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<Target Name="BeforeBuild">
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</Target>
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<Target Name="AfterBuild">
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</Target>
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</Project>
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</Project>

‎EngineLayer/Mods/f.txt

+1-9
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Fixed modifications
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ID Carbamidomethyl
3-
FT MOD_RES
43
TG Cysteine
54
PP Anywhere.
65
MM 57.02146373
76
CF H3 C2 N O
8-
//
9-
ID tmt
10-
FT MOD_RES
11-
TG Any
12-
PP Peptide N-terminal.
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MM 57.02146373
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CF H3 C2 N O
15-
//
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//

‎EngineLayer/Mods/tmt.txt

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ID TMT_tag_lysine
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TG Lysine
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PP Anywhere.
5+
MM 229.1629321568
6+
//
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ID TMT_tag_terminal
8+
TG X
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PP Peptide N-terminal.
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MM 229.1629321568
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//

‎EngineLayer/packages.config

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<?xml version="1.0" encoding="utf-8"?>
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<packages>
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<package id="MathNet.Numerics" version="3.17.0" targetFramework="net451" />
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<package id="mzLib" version="1.0.129" targetFramework="net451" />
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<package id="mzLib" version="1.0.131" targetFramework="net451" />
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<package id="Zlib.Portable" version="1.11.0" targetFramework="net451" />
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</packages>

‎GUI/GUI.csproj

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<TreatWarningsAsErrors>true</TreatWarningsAsErrors>
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</PropertyGroup>
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<ItemGroup>
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<Reference Include="Chemistry, Version=1.0.129.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.129\lib\Chemistry.dll</HintPath>
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<Reference Include="Chemistry, Version=1.0.131.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.131\lib\Chemistry.dll</HintPath>
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</Reference>
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<Reference Include="ManagedThermoHelperLayer, Version=1.0.129.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.129\lib\ManagedThermoHelperLayer.dll</HintPath>
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<Reference Include="ManagedThermoHelperLayer, Version=1.0.131.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.131\lib\ManagedThermoHelperLayer.dll</HintPath>
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</Reference>
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<Reference Include="MassSpectrometry, Version=1.0.129.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.129\lib\MassSpectrometry.dll</HintPath>
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<Reference Include="MassSpectrometry, Version=1.0.131.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.131\lib\MassSpectrometry.dll</HintPath>
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</Reference>
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<Reference Include="MathNet.Numerics, Version=3.17.0.0, Culture=neutral, processorArchitecture=MSIL">
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<HintPath>..\packages\MathNet.Numerics.3.17.0\lib\net40\MathNet.Numerics.dll</HintPath>
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<Private>True</Private>
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</Reference>
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<Reference Include="mzIdentML, Version=1.0.129.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.129\lib\mzIdentML.dll</HintPath>
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<Reference Include="mzIdentML, Version=1.0.131.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.131\lib\mzIdentML.dll</HintPath>
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</Reference>
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<Reference Include="MzLibUtil, Version=1.0.129.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.129\lib\MzLibUtil.dll</HintPath>
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<Reference Include="MzLibUtil, Version=1.0.131.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.131\lib\MzLibUtil.dll</HintPath>
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</Reference>
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<Reference Include="MzML, Version=1.0.129.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.129\lib\MzML.dll</HintPath>
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<Reference Include="MzML, Version=1.0.131.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.131\lib\MzML.dll</HintPath>
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</Reference>
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<Reference Include="Proteomics, Version=1.0.129.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.129\lib\Proteomics.dll</HintPath>
64+
<Reference Include="Proteomics, Version=1.0.131.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.131\lib\Proteomics.dll</HintPath>
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</Reference>
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<Reference Include="Spectra, Version=1.0.129.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.129\lib\Spectra.dll</HintPath>
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<Reference Include="Spectra, Version=1.0.131.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.131\lib\Spectra.dll</HintPath>
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</Reference>
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<Reference Include="System" />
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<Reference Include="System.Data" />
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<Reference Include="System.Xaml">
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<RequiredTargetFramework>4.0</RequiredTargetFramework>
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</Reference>
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<Reference Include="Thermo, Version=1.0.129.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.129\lib\Thermo.dll</HintPath>
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<Reference Include="Thermo, Version=1.0.131.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.131\lib\Thermo.dll</HintPath>
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</Reference>
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<Reference Include="UsefulProteomicsDatabases, Version=1.0.129.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.129\lib\UsefulProteomicsDatabases.dll</HintPath>
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<Reference Include="UsefulProteomicsDatabases, Version=1.0.131.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.131\lib\UsefulProteomicsDatabases.dll</HintPath>
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</Reference>
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<Reference Include="WindowsBase" />
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<Reference Include="PresentationCore" />
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</ProjectReference>
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</ItemGroup>
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<Import Project="$(MSBuildToolsPath)\Microsoft.CSharp.targets" />
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<Import Project="..\packages\mzLib.1.0.129\build\mzLib.targets" Condition="Exists('..\packages\mzLib.1.0.129\build\mzLib.targets')" />
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<Import Project="..\packages\mzLib.1.0.131\build\mzLib.targets" Condition="Exists('..\packages\mzLib.1.0.131\build\mzLib.targets')" />
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<Target Name="EnsureNuGetPackageBuildImports" BeforeTargets="PrepareForBuild">
195+
<PropertyGroup>
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<ErrorText>This project references NuGet package(s) that are missing on this computer. Use NuGet Package Restore to download them. For more information, see http://go.microsoft.com/fwlink/?LinkID=322105. The missing file is {0}.</ErrorText>
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</PropertyGroup>
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<Error Condition="!Exists('..\packages\mzLib.1.0.131\build\mzLib.targets')" Text="$([System.String]::Format('$(ErrorText)', '..\packages\mzLib.1.0.131\build\mzLib.targets'))" />
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</Target>
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<!-- To modify your build process, add your task inside one of the targets below and uncomment it.
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Other similar extension points exist, see Microsoft.Common.targets.
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<Target Name="BeforeBuild">
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</Target>
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</Project>
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</Project>

‎GUI/packages.config

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@@ -1,6 +1,6 @@
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<?xml version="1.0" encoding="utf-8"?>
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<packages>
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<package id="MathNet.Numerics" version="3.17.0" targetFramework="net451" />
4-
<package id="mzLib" version="1.0.129" targetFramework="net451" />
4+
<package id="mzLib" version="1.0.131" targetFramework="net451" />
55
<package id="Zlib.Portable" version="1.11.0" targetFramework="net451" />
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</packages>

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