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stefanks
authored
Merge pull request #171 from smith-chem-wisc/StefanBranch
release for rachel
2 parents ec26760 + 84e3fd9 commit f6164f1

21 files changed

+232
-188
lines changed

‎InternalLogic/InternalLogicEngineLayer.csproj

+32-24
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@@ -34,10 +34,34 @@
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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=1.0.73.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.73\lib\Chemistry.dll</HintPath>
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<Private>True</Private>
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</Reference>
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<Reference Include="MassSpectrometry, Version=1.0.73.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.73\lib\MassSpectrometry.dll</HintPath>
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<Private>True</Private>
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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=1.0.73.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.73\lib\mzIdentML.dll</HintPath>
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<Private>True</Private>
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</Reference>
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<Reference Include="MzML, Version=1.0.73.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.73\lib\MzML.dll</HintPath>
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<Private>True</Private>
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</Reference>
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<Reference Include="Proteomics, Version=1.0.73.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.73\lib\Proteomics.dll</HintPath>
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<Private>True</Private>
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</Reference>
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<Reference Include="Spectra, Version=1.0.73.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.73\lib\Spectra.dll</HintPath>
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<Private>True</Private>
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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.Xml.Linq" />
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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="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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<Reference Include="Thermo, Version=1.0.73.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.73\lib\Thermo.dll</HintPath>
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<Private>True</Private>
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</Reference>
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<Reference Include="Chemistry">
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<HintPath>..\packages\mzLib.1.0.72\lib\Chemistry.dll</HintPath>
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</Reference>
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<Reference Include="MassSpectrometry">
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<HintPath>..\packages\mzLib.1.0.72\lib\MassSpectrometry.dll</HintPath>
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</Reference>
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<Reference Include="mzIdentML">
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<HintPath>..\packages\mzLib.1.0.72\lib\mzIdentML.dll</HintPath>
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</Reference>
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<Reference Include="MzML">
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<HintPath>..\packages\mzLib.1.0.72\lib\MzML.dll</HintPath>
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</Reference>
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<Reference Include="Proteomics">
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<HintPath>..\packages\mzLib.1.0.72\lib\Proteomics.dll</HintPath>
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</Reference>
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<Reference Include="Spectra">
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<HintPath>..\packages\mzLib.1.0.72\lib\Spectra.dll</HintPath>
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</Reference>
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<Reference Include="Thermo">
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<HintPath>..\packages\mzLib.1.0.72\lib\Thermo.dll</HintPath>
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<Reference Include="UsefulProteomicsDatabases, Version=1.0.73.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.73\lib\UsefulProteomicsDatabases.dll</HintPath>
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<Private>True</Private>
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</Reference>
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<Reference Include="UsefulProteomicsDatabases">
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<HintPath>..\packages\mzLib.1.0.72\lib\UsefulProteomicsDatabases.dll</HintPath>
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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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<Private>True</Private>
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</Reference>
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</ItemGroup>
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<ItemGroup>

‎InternalLogic/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="1.0.72" targetFramework="net451" />
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<package id="mzLib" version="1.0.73" targetFramework="net451" />
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<package id="Zlib.Portable" version="1.11.0" targetFramework="net451" />
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</packages>

‎InternalLogicWithFileIO/InternalLogicTaskLayer.csproj

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@@ -34,14 +34,38 @@
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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=1.0.73.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.73\lib\Chemistry.dll</HintPath>
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<Private>True</Private>
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</Reference>
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<Reference Include="MassSpectrometry, Version=1.0.73.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.73\lib\MassSpectrometry.dll</HintPath>
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<Private>True</Private>
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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=1.0.73.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.73\lib\mzIdentML.dll</HintPath>
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<Private>True</Private>
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</Reference>
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<Reference Include="MzML, Version=1.0.73.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.73\lib\MzML.dll</HintPath>
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<Private>True</Private>
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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=1.0.73.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.73\lib\Proteomics.dll</HintPath>
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<Private>True</Private>
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</Reference>
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<Reference Include="Spectra, Version=1.0.73.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.73\lib\Spectra.dll</HintPath>
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<Private>True</Private>
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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.Xml.Linq" />
@@ -50,33 +74,17 @@
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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="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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<Reference Include="Thermo, Version=1.0.73.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.73\lib\Thermo.dll</HintPath>
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<Private>True</Private>
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</Reference>
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<Reference Include="Chemistry">
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<HintPath>..\packages\mzLib.1.0.72\lib\Chemistry.dll</HintPath>
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</Reference>
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<Reference Include="MassSpectrometry">
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<HintPath>..\packages\mzLib.1.0.72\lib\MassSpectrometry.dll</HintPath>
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</Reference>
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<Reference Include="mzIdentML">
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<HintPath>..\packages\mzLib.1.0.72\lib\mzIdentML.dll</HintPath>
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</Reference>
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<Reference Include="MzML">
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<HintPath>..\packages\mzLib.1.0.72\lib\MzML.dll</HintPath>
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</Reference>
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<Reference Include="Proteomics">
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<HintPath>..\packages\mzLib.1.0.72\lib\Proteomics.dll</HintPath>
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</Reference>
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<Reference Include="Spectra">
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<HintPath>..\packages\mzLib.1.0.72\lib\Spectra.dll</HintPath>
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</Reference>
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<Reference Include="Thermo">
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<HintPath>..\packages\mzLib.1.0.72\lib\Thermo.dll</HintPath>
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<Reference Include="UsefulProteomicsDatabases, Version=1.0.73.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.73\lib\UsefulProteomicsDatabases.dll</HintPath>
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<Private>True</Private>
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</Reference>
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<Reference Include="UsefulProteomicsDatabases">
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<HintPath>..\packages\mzLib.1.0.72\lib\UsefulProteomicsDatabases.dll</HintPath>
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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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<Private>True</Private>
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</Reference>
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</ItemGroup>
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<ItemGroup>

‎InternalLogicWithFileIO/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="1.0.72" targetFramework="net451" />
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<package id="mzLib" version="1.0.73" 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>

‎MetaMorpheusCommandLine/MetaMorpheusCommandLine.csproj

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@@ -35,14 +35,38 @@
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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=1.0.73.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.73\lib\Chemistry.dll</HintPath>
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<Private>True</Private>
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</Reference>
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<Reference Include="MassSpectrometry, Version=1.0.73.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.73\lib\MassSpectrometry.dll</HintPath>
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<Private>True</Private>
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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=1.0.73.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.73\lib\mzIdentML.dll</HintPath>
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<Private>True</Private>
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</Reference>
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<Reference Include="MzML, Version=1.0.73.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.73\lib\MzML.dll</HintPath>
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<Private>True</Private>
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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=1.0.73.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.73\lib\Proteomics.dll</HintPath>
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<Private>True</Private>
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</Reference>
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<Reference Include="Spectra, Version=1.0.73.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.73\lib\Spectra.dll</HintPath>
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<Private>True</Private>
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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.Numerics" />
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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="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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<Reference Include="Thermo, Version=1.0.73.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.73\lib\Thermo.dll</HintPath>
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<Private>True</Private>
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</Reference>
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<Reference Include="Chemistry">
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<HintPath>..\packages\mzLib.1.0.72\lib\Chemistry.dll</HintPath>
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</Reference>
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<Reference Include="MassSpectrometry">
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<HintPath>..\packages\mzLib.1.0.72\lib\MassSpectrometry.dll</HintPath>
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</Reference>
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<Reference Include="mzIdentML">
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<HintPath>..\packages\mzLib.1.0.72\lib\mzIdentML.dll</HintPath>
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</Reference>
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<Reference Include="MzML">
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<HintPath>..\packages\mzLib.1.0.72\lib\MzML.dll</HintPath>
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</Reference>
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<Reference Include="Proteomics">
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<HintPath>..\packages\mzLib.1.0.72\lib\Proteomics.dll</HintPath>
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</Reference>
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<Reference Include="Spectra">
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<HintPath>..\packages\mzLib.1.0.72\lib\Spectra.dll</HintPath>
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</Reference>
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<Reference Include="Thermo">
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<HintPath>..\packages\mzLib.1.0.72\lib\Thermo.dll</HintPath>
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<Reference Include="UsefulProteomicsDatabases, Version=1.0.73.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.73\lib\UsefulProteomicsDatabases.dll</HintPath>
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<Private>True</Private>
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</Reference>
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<Reference Include="UsefulProteomicsDatabases">
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<HintPath>..\packages\mzLib.1.0.72\lib\UsefulProteomicsDatabases.dll</HintPath>
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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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<Private>True</Private>
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</Reference>
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</ItemGroup>
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<ItemGroup>

‎MetaMorpheusCommandLine/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" />
4-
<package id="mzLib" version="1.0.72" targetFramework="net451" />
4+
<package id="mzLib" version="1.0.73" 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>

‎MetaMorpheusGUI/MainWindow.xaml.cs

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modListObservableCollection.Add(new ModList("ptmlist.txt"));
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modListObservableCollection.Add(new ModList("m.txt"));
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modListObservableCollection.Add(new ModList("glyco.txt"));
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modListObservableCollection.Add(new ModList("r.txt"));
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modListObservableCollection.Add(new ModList("s.txt"));
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//modListObservableCollection.Add(new ModList("r.txt"));
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//modListObservableCollection.Add(new ModList("s.txt"));
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LoadSearchModesFromFile();
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‎MetaMorpheusGUI/MetaMorpheusGUI.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=1.0.72.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.72\lib\Chemistry.dll</HintPath>
40+
<Reference Include="Chemistry, Version=1.0.73.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.73\lib\Chemistry.dll</HintPath>
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<Private>True</Private>
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</Reference>
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<Reference Include="MassSpectrometry, Version=1.0.72.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.72\lib\MassSpectrometry.dll</HintPath>
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<Reference Include="MassSpectrometry, Version=1.0.73.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.73\lib\MassSpectrometry.dll</HintPath>
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<Private>True</Private>
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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=1.0.72.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.72\lib\mzIdentML.dll</HintPath>
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<Reference Include="mzIdentML, Version=1.0.73.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.73\lib\mzIdentML.dll</HintPath>
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<Private>True</Private>
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</Reference>
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<Reference Include="MzML, Version=1.0.72.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.72\lib\MzML.dll</HintPath>
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<Reference Include="MzML, Version=1.0.73.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.73\lib\MzML.dll</HintPath>
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<Private>True</Private>
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</Reference>
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<Reference Include="Proteomics, Version=1.0.72.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.72\lib\Proteomics.dll</HintPath>
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<Reference Include="Proteomics, Version=1.0.73.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.73\lib\Proteomics.dll</HintPath>
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<Private>True</Private>
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</Reference>
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<Reference Include="Spectra, Version=1.0.72.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.72\lib\Spectra.dll</HintPath>
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<Reference Include="Spectra, Version=1.0.73.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.73\lib\Spectra.dll</HintPath>
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<Private>True</Private>
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</Reference>
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<Reference Include="System" />
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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=1.0.72.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.72\lib\Thermo.dll</HintPath>
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<Reference Include="Thermo, Version=1.0.73.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.73\lib\Thermo.dll</HintPath>
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<Private>True</Private>
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</Reference>
84-
<Reference Include="UsefulProteomicsDatabases, Version=1.0.72.0, Culture=neutral, processorArchitecture=AMD64">
85-
<HintPath>..\packages\mzLib.1.0.72\lib\UsefulProteomicsDatabases.dll</HintPath>
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<Reference Include="UsefulProteomicsDatabases, Version=1.0.73.0, Culture=neutral, processorArchitecture=AMD64">
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<HintPath>..\packages\mzLib.1.0.73\lib\UsefulProteomicsDatabases.dll</HintPath>
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<Private>True</Private>
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</Reference>
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<Reference Include="WindowsBase" />

‎MetaMorpheusGUI/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="1.0.72" targetFramework="net451" />
4+
<package id="mzLib" version="1.0.73" targetFramework="net451" />
55
<package id="Zlib.Portable" version="1.11.0" targetFramework="net451" />
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</packages>

‎OldInternalLogic/MorpheusModification.cs

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@@ -6,13 +6,12 @@ public class MorpheusModification
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{
77
#region Public Constructors
88

9-
public MorpheusModification(string nameInXml, ModificationType type, char aminoAcid, double monoisotopicMassShift,
10-
string database, string databaseName, char prevAA, double alternativeMassShift, bool labile, ChemicalFormula cf)
9+
public MorpheusModification(string nameInXml, ModificationType type, char aminoAcid, string database, string databaseName, char prevAA, double alternativeMassShift, bool labile, ChemicalFormula cf)
1110
{
1211
this.NameInXml = nameInXml;
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ThisModificationType = type;
1413
AminoAcid = aminoAcid;
15-
MonoisotopicMassShift = monoisotopicMassShift;
14+
MonoisotopicMassShift = cf.MonoisotopicMass;
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Database = database;
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DatabaseName = databaseName;
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PrevAminoAcid = prevAA;
@@ -26,6 +25,14 @@ public MorpheusModification(string NameInXml)
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this.NameInXml = NameInXml;
2726
}
2827

28+
public MorpheusModification(double v)
29+
{
30+
this.MonoisotopicMassShift = v;
31+
ThisModificationType = ModificationType.AminoAcidResidue;
32+
PrevAminoAcid = '\0';
33+
this.NameInXml = "";
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}
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2936
#endregion Public Constructors
3037

3138
#region Public Properties
@@ -60,4 +67,4 @@ public override string ToString()
6067

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#endregion Public Methods
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}
63-
}
70+
}

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