update mzLib and finalize Variant results summary (#1742)

* update mzLib and finalize results summary * update unit testing * update testing take 2 * "group" fdr explicitly stated * addressing reviewer comments * Modification on variatn site edit * comment added * Flexibility of FDR filter
smith-chem-wisc · Oct 25, 2019 · 3e67e3a · 3e67e3a
1 parent 8c5fddf
commit 3e67e3a
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diff --git a/CMD/CMD.csproj b/CMD/CMD.csproj
@@ -10,7 +10,7 @@
     <PackageReference Include="FluentCommandLineParser" Version="1.4.3" />
     <PackageReference Include="Microsoft.ML" Version="1.1.0" />
     <PackageReference Include="Microsoft.ML.FastTree" Version="1.1.0" />
-    <PackageReference Include="mzLib" Version="1.0.454" />
+    <PackageReference Include="mzLib" Version="1.0.459" />
     <PackageReference Include="Nett" Version="0.8.0" />
     <PackageReference Include="SharpLearning.Common.Interfaces" Version="0.26.9" />
     <PackageReference Include="SharpLearning.Containers" Version="0.26.9" />

diff --git a/EngineLayer/EngineLayer.csproj b/EngineLayer/EngineLayer.csproj
@@ -11,7 +11,7 @@
     <PackageReference Include="Accord.Statistics" Version="3.8.0" />
     <PackageReference Include="Microsoft.ML" Version="1.1.0" />
     <PackageReference Include="Microsoft.ML.FastTree" Version="1.1.0" />
-    <PackageReference Include="mzLib" Version="1.0.454" />
+    <PackageReference Include="mzLib" Version="1.0.459" />
     <PackageReference Include="Nett" Version="0.8.0" />
     <PackageReference Include="Newtonsoft.Json" Version="11.0.1" />
     <PackageReference Include="SharpLearning.Common.Interfaces" Version="0.26.9" />

diff --git a/GUI/GUI.csproj b/GUI/GUI.csproj
@@ -78,26 +78,26 @@
   </PropertyGroup>
   <ItemGroup>
     <Reference Include="BayesianEstimation, Version=1.0.0.0, Culture=neutral, processorArchitecture=AMD64">
-      <HintPath>..\packages\mzLib.1.0.454\lib\net471\BayesianEstimation.dll</HintPath>
+      <HintPath>..\packages\mzLib.1.0.459\lib\net471\BayesianEstimation.dll</HintPath>
     </Reference>
     <Reference Include="Chemistry, Version=1.0.0.0, Culture=neutral, processorArchitecture=AMD64">
-      <HintPath>..\packages\mzLib.1.0.454\lib\net471\Chemistry.dll</HintPath>
+      <HintPath>..\packages\mzLib.1.0.459\lib\net471\Chemistry.dll</HintPath>
     </Reference>
     <Reference Include="FlashLFQ, Version=1.0.0.0, Culture=neutral, processorArchitecture=AMD64">
-      <HintPath>..\packages\mzLib.1.0.454\lib\net471\FlashLFQ.dll</HintPath>
+      <HintPath>..\packages\mzLib.1.0.459\lib\net471\FlashLFQ.dll</HintPath>
     </Reference>
     <Reference Include="itextsharp, Version=5.5.13.0, Culture=neutral, PublicKeyToken=8354ae6d2174ddca, processorArchitecture=MSIL">
       <HintPath>..\packages\iTextSharp.5.5.13\lib\itextsharp.dll</HintPath>
     </Reference>
     <Reference Include="MassSpectrometry, Version=1.0.0.0, Culture=neutral, processorArchitecture=AMD64">
-      <HintPath>..\packages\mzLib.1.0.454\lib\net471\MassSpectrometry.dll</HintPath>
+      <HintPath>..\packages\mzLib.1.0.459\lib\net471\MassSpectrometry.dll</HintPath>
     </Reference>
     <Reference Include="MathNet.Numerics, Version=4.8.1.0, Culture=neutral, processorArchitecture=MSIL">
       <HintPath>..\packages\MathNet.Numerics.4.8.1\lib\net461\MathNet.Numerics.dll</HintPath>
       <Private>True</Private>
     </Reference>
     <Reference Include="Mgf, Version=1.0.0.0, Culture=neutral, processorArchitecture=AMD64">
-      <HintPath>..\packages\mzLib.1.0.454\lib\net471\Mgf.dll</HintPath>
+      <HintPath>..\packages\mzLib.1.0.459\lib\net471\Mgf.dll</HintPath>
     </Reference>
     <Reference Include="Microsoft.ML.Core, Version=1.0.0.0, Culture=neutral, PublicKeyToken=cc7b13ffcd2ddd51, processorArchitecture=MSIL">
       <HintPath>..\packages\Microsoft.ML.1.1.0\lib\netstandard2.0\Microsoft.ML.Core.dll</HintPath>
@@ -127,13 +127,13 @@
       <HintPath>..\packages\Microsoft.ML.1.1.0\lib\netstandard2.0\Microsoft.ML.Transforms.dll</HintPath>
     </Reference>
     <Reference Include="MzIdentML, Version=1.0.0.0, Culture=neutral, processorArchitecture=AMD64">
-      <HintPath>..\packages\mzLib.1.0.454\lib\net471\MzIdentML.dll</HintPath>
+      <HintPath>..\packages\mzLib.1.0.459\lib\net471\MzIdentML.dll</HintPath>
     </Reference>
     <Reference Include="MzLibUtil, Version=1.0.0.0, Culture=neutral, processorArchitecture=AMD64">
-      <HintPath>..\packages\mzLib.1.0.454\lib\net471\MzLibUtil.dll</HintPath>
+      <HintPath>..\packages\mzLib.1.0.459\lib\net471\MzLibUtil.dll</HintPath>
     </Reference>
     <Reference Include="MzML, Version=1.0.0.0, Culture=neutral, processorArchitecture=AMD64">
-      <HintPath>..\packages\mzLib.1.0.454\lib\net471\MzML.dll</HintPath>
+      <HintPath>..\packages\mzLib.1.0.459\lib\net471\MzML.dll</HintPath>
     </Reference>
     <Reference Include="Nett, Version=0.8.0.0, Culture=neutral, processorArchitecture=MSIL">
       <HintPath>..\packages\Nett.0.8.0\lib\Net40\Nett.dll</HintPath>
@@ -148,10 +148,10 @@
       <HintPath>..\packages\OxyPlot.Wpf.1.0.0\lib\net45\OxyPlot.Wpf.dll</HintPath>
     </Reference>
     <Reference Include="PepXML, Version=1.0.0.0, Culture=neutral, processorArchitecture=AMD64">
-      <HintPath>..\packages\mzLib.1.0.454\lib\net471\PepXML.dll</HintPath>
+      <HintPath>..\packages\mzLib.1.0.459\lib\net471\PepXML.dll</HintPath>
     </Reference>
     <Reference Include="Proteomics, Version=1.0.0.0, Culture=neutral, processorArchitecture=AMD64">
-      <HintPath>..\packages\mzLib.1.0.454\lib\net471\Proteomics.dll</HintPath>
+      <HintPath>..\packages\mzLib.1.0.459\lib\net471\Proteomics.dll</HintPath>
     </Reference>
     <Reference Include="SharpLearning.Common.Interfaces, Version=0.26.9.0, Culture=neutral, processorArchitecture=MSIL">
       <HintPath>..\packages\SharpLearning.Common.Interfaces.0.26.9\lib\net461\SharpLearning.Common.Interfaces.dll</HintPath>
@@ -216,22 +216,22 @@
     </Reference>
     <Reference Include="System.Xml" />
     <Reference Include="ThermoFisher.CommonCore.BackgroundSubtraction, Version=1.0.0.0, Culture=neutral, PublicKeyToken=1aef06afb5abd953, processorArchitecture=MSIL">
-      <HintPath>..\packages\mzLib.1.0.454\lib\net471\ThermoFisher.CommonCore.BackgroundSubtraction.dll</HintPath>
+      <HintPath>..\packages\mzLib.1.0.459\lib\net471\ThermoFisher.CommonCore.BackgroundSubtraction.dll</HintPath>
     </Reference>
     <Reference Include="ThermoFisher.CommonCore.Data, Version=1.0.0.0, Culture=neutral, PublicKeyToken=1aef06afb5abd953, processorArchitecture=MSIL">
-      <HintPath>..\packages\mzLib.1.0.454\lib\net471\ThermoFisher.CommonCore.Data.dll</HintPath>
+      <HintPath>..\packages\mzLib.1.0.459\lib\net471\ThermoFisher.CommonCore.Data.dll</HintPath>
     </Reference>
     <Reference Include="ThermoFisher.CommonCore.MassPrecisionEstimator, Version=1.0.0.0, Culture=neutral, processorArchitecture=MSIL">
-      <HintPath>..\packages\mzLib.1.0.454\lib\net471\ThermoFisher.CommonCore.MassPrecisionEstimator.dll</HintPath>
+      <HintPath>..\packages\mzLib.1.0.459\lib\net471\ThermoFisher.CommonCore.MassPrecisionEstimator.dll</HintPath>
     </Reference>
     <Reference Include="ThermoFisher.CommonCore.RawFileReader, Version=1.0.0.0, Culture=neutral, PublicKeyToken=1aef06afb5abd953, processorArchitecture=MSIL">
-      <HintPath>..\packages\mzLib.1.0.454\lib\net471\ThermoFisher.CommonCore.RawFileReader.dll</HintPath>
+      <HintPath>..\packages\mzLib.1.0.459\lib\net471\ThermoFisher.CommonCore.RawFileReader.dll</HintPath>
     </Reference>
     <Reference Include="ThermoRawFileReader, Version=1.0.0.0, Culture=neutral, processorArchitecture=AMD64">
-      <HintPath>..\packages\mzLib.1.0.454\lib\net471\ThermoRawFileReader.dll</HintPath>
+      <HintPath>..\packages\mzLib.1.0.459\lib\net471\ThermoRawFileReader.dll</HintPath>
     </Reference>
     <Reference Include="UsefulProteomicsDatabases, Version=1.0.0.0, Culture=neutral, processorArchitecture=MSIL">
-      <HintPath>..\packages\mzLib.1.0.454\lib\net471\UsefulProteomicsDatabases.dll</HintPath>
+      <HintPath>..\packages\mzLib.1.0.459\lib\net471\UsefulProteomicsDatabases.dll</HintPath>
     </Reference>
     <Reference Include="WindowsBase" />
     <Reference Include="PresentationCore" />
@@ -497,8 +497,8 @@
       <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>
     </PropertyGroup>
     <Error Condition="!Exists('..\packages\MathNet.Numerics.MKL.Win.2.2.0\build\MathNet.Numerics.MKL.Win.targets')" Text="$([System.String]::Format('$(ErrorText)', '..\packages\MathNet.Numerics.MKL.Win.2.2.0\build\MathNet.Numerics.MKL.Win.targets'))" />
-    <Error Condition="!Exists('..\packages\mzLib.1.0.454\build\net471\mzLib.targets')" Text="$([System.String]::Format('$(ErrorText)', '..\packages\mzLib.1.0.454\build\net471\mzLib.targets'))" />
+    <Error Condition="!Exists('..\packages\mzLib.1.0.459\build\net471\mzLib.targets')" Text="$([System.String]::Format('$(ErrorText)', '..\packages\mzLib.1.0.459\build\net471\mzLib.targets'))" />
   </Target>
   <Import Project="..\packages\MathNet.Numerics.MKL.Win.2.2.0\build\MathNet.Numerics.MKL.Win.targets" Condition="Exists('..\packages\MathNet.Numerics.MKL.Win.2.2.0\build\MathNet.Numerics.MKL.Win.targets')" />
-  <Import Project="..\packages\mzLib.1.0.454\build\net471\mzLib.targets" Condition="Exists('..\packages\mzLib.1.0.454\build\net471\mzLib.targets')" />
+  <Import Project="..\packages\mzLib.1.0.459\build\net471\mzLib.targets" Condition="Exists('..\packages\mzLib.1.0.459\build\net471\mzLib.targets')" />
 </Project>
diff --git a/GUI/packages.config b/GUI/packages.config
@@ -7,7 +7,7 @@
   <package id="Microsoft.ML.CpuMath" version="1.1.0" targetFramework="net471" />
   <package id="Microsoft.ML.DataView" version="1.1.0" targetFramework="net471" />
   <package id="Microsoft.ML.FastTree" version="1.1.0" targetFramework="net471" />
-  <package id="mzLib" version="1.0.454" targetFramework="net471" />
+  <package id="mzLib" version="1.0.459" targetFramework="net471" />
   <package id="Nett" version="0.8.0" targetFramework="net471" />
   <package id="Newtonsoft.Json" version="11.0.1" targetFramework="net471" />
   <package id="OxyPlot.Core" version="1.0.0" targetFramework="net471" />