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stefanks
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Merge pull request #260 from smith-chem-wisc/StefanBranch
Stefan branch
2 parents f5a27d0 + b7e2eb1 commit 0debc43

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-265
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20 files changed

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-265
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‎CMD/CMD.csproj‎

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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=1.0.131.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.131\lib\Chemistry.dll</HintPath>
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<Reference Include="Chemistry, Version=1.0.132.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.132\lib\Chemistry.dll</HintPath>
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</Reference>
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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 Include="ManagedThermoHelperLayer, Version=1.0.132.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.132\lib\ManagedThermoHelperLayer.dll</HintPath>
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</Reference>
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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 Include="MassSpectrometry, Version=1.0.132.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.132\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=1.0.131.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.131\lib\mzIdentML.dll</HintPath>
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<Reference Include="mzIdentML, Version=1.0.132.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.132\lib\mzIdentML.dll</HintPath>
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</Reference>
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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 Include="MzLibUtil, Version=1.0.132.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.132\lib\MzLibUtil.dll</HintPath>
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</Reference>
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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 Include="MzML, Version=1.0.132.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.132\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=1.0.131.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.131\lib\Proteomics.dll</HintPath>
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<Reference Include="Proteomics, Version=1.0.132.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.132\lib\Proteomics.dll</HintPath>
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</Reference>
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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 Include="Spectra, Version=1.0.132.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.132\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=1.0.131.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.131\lib\Thermo.dll</HintPath>
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<Reference Include="Thermo, Version=1.0.132.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.132\lib\Thermo.dll</HintPath>
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</Reference>
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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 Include="UsefulProteomicsDatabases, Version=1.0.132.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.132\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="$(MSBuildToolsPath)\Microsoft.CSharp.targets" />
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<Import Project="..\packages\mzLib.1.0.131\build\mzLib.targets" Condition="Exists('..\packages\mzLib.1.0.131\build\mzLib.targets')" />
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<Import Project="..\packages\mzLib.1.0.132\build\mzLib.targets" Condition="Exists('..\packages\mzLib.1.0.132\build\mzLib.targets')" />
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<Target Name="EnsureNuGetPackageBuildImports" BeforeTargets="PrepareForBuild">
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<PropertyGroup>
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<ErrorText>This project references NuGet package(s) that are missing on this computer. Use NuGet Package Restore to download them. For more information, see http://go.microsoft.com/fwlink/?LinkID=322105. The missing file is {0}.</ErrorText>
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</PropertyGroup>
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<Error Condition="!Exists('..\packages\mzLib.1.0.131\build\mzLib.targets')" Text="$([System.String]::Format('$(ErrorText)', '..\packages\mzLib.1.0.131\build\mzLib.targets'))" />
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<Error Condition="!Exists('..\packages\mzLib.1.0.132\build\mzLib.targets')" Text="$([System.String]::Format('$(ErrorText)', '..\packages\mzLib.1.0.132\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.

‎CMD/packages.config‎

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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" />
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<package id="mzLib" version="1.0.131" targetFramework="net451" />
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<package id="mzLib" version="1.0.132" 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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@@ -36,33 +36,33 @@
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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=1.0.131.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.131\lib\Chemistry.dll</HintPath>
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<Reference Include="Chemistry, Version=1.0.132.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.132\lib\Chemistry.dll</HintPath>
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</Reference>
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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 Include="ManagedThermoHelperLayer, Version=1.0.132.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.132\lib\ManagedThermoHelperLayer.dll</HintPath>
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</Reference>
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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 Include="MassSpectrometry, Version=1.0.132.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.132\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=1.0.131.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.131\lib\mzIdentML.dll</HintPath>
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<Reference Include="mzIdentML, Version=1.0.132.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.132\lib\mzIdentML.dll</HintPath>
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</Reference>
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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 Include="MzLibUtil, Version=1.0.132.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.132\lib\MzLibUtil.dll</HintPath>
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</Reference>
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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 Include="MzML, Version=1.0.132.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.132\lib\MzML.dll</HintPath>
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</Reference>
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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 Include="Proteomics, Version=1.0.132.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.132\lib\Proteomics.dll</HintPath>
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</Reference>
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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 Include="Spectra, Version=1.0.132.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.132\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=1.0.131.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.131\lib\Thermo.dll</HintPath>
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<Reference Include="Thermo, Version=1.0.132.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.132\lib\Thermo.dll</HintPath>
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</Reference>
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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 Include="UsefulProteomicsDatabases, Version=1.0.132.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.132\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 Include="Mods\f.txt">
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<CopyToOutputDirectory>Always</CopyToOutputDirectory>
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</Content>
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<Content Include="Mods\fNew.txt">
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<CopyToOutputDirectory>Always</CopyToOutputDirectory>
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</Content>
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<Content Include="Mods\glyco.txt">
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<CopyToOutputDirectory>Always</CopyToOutputDirectory>
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</Content>
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</Content>
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</ItemGroup>
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<Import Project="$(MSBuildToolsPath)\Microsoft.CSharp.targets" />
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<Import Project="..\packages\mzLib.1.0.131\build\mzLib.targets" Condition="Exists('..\packages\mzLib.1.0.131\build\mzLib.targets')" />
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<Import Project="..\packages\mzLib.1.0.132\build\mzLib.targets" Condition="Exists('..\packages\mzLib.1.0.132\build\mzLib.targets')" />
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<Target Name="EnsureNuGetPackageBuildImports" BeforeTargets="PrepareForBuild">
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<PropertyGroup>
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<ErrorText>This project references NuGet package(s) that are missing on this computer. Use NuGet Package Restore to download them. For more information, see http://go.microsoft.com/fwlink/?LinkID=322105. The missing file is {0}.</ErrorText>
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</PropertyGroup>
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<Error Condition="!Exists('..\packages\mzLib.1.0.131\build\mzLib.targets')" Text="$([System.String]::Format('$(ErrorText)', '..\packages\mzLib.1.0.131\build\mzLib.targets'))" />
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<Error Condition="!Exists('..\packages\mzLib.1.0.132\build\mzLib.targets')" Text="$([System.String]::Format('$(ErrorText)', '..\packages\mzLib.1.0.132\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.

‎EngineLayer/Gptmd/GptmdResults.cs‎

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using Proteomics;
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using System;
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using System.Collections.Generic;
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using System.Linq;
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using System.Text;
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namespace EngineLayer.Gptmd
@@ -30,18 +31,20 @@ public GptmdResults(MyEngine s, Dictionary<string, HashSet<Tuple<int, Modificati
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#endregion Public Properties
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#region Protected Properties
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#region Public Methods
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public override string ToString()
3637
{
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var sb = new StringBuilder();
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sb.AppendLine(base.ToString());
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sb.AppendLine("Modifications added = " + modsAdded);
40-
sb.Append("Proteins expanded = " + Mods.Count);
41+
sb.AppendLine("Proteins expanded = " + Mods.Count);
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sb.AppendLine("Mods added types and counts:");
43+
sb.Append(string.Join(Environment.NewLine, Mods.SelectMany(b => b.Value).GroupBy(b => b.Item2).OrderBy(b => -b.Count()).Select(b => b.Key.id + " " + b.Count())));
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return sb.ToString();
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}
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#endregion Protected Properties
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#endregion Public Methods
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}
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}

‎EngineLayer/Mods/f.txt‎

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Fixed modifications
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ID Carbamidomethyl
3-
TG Cysteine
3+
TG C
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PP Anywhere.
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MM 57.02146373
6+
MT FixedMod
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CF H3 C2 N O
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//

‎EngineLayer/Mods/fNew.txt‎

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This file was deleted.

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