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[WIP] Remove decoys identical to targets #2393

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[WIP] Remove decoys identical to targets #2393

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ce17fe1
update csproj
trishorts Jul 29, 2024
3ce6c53
nuget update
trishorts Jul 29, 2024
7964dc8
lets start here
trishorts Jul 29, 2024
961164b
it ran bro
trishorts Jul 29, 2024
38f6779
fsad
trishorts Jul 29, 2024
b89012d
remove ostensibly unused dlls
trishorts Jul 29, 2024
82449d5
bouncy castle linked to itext for writing pdf
trishorts Jul 29, 2024
be7295d
unused using
trishorts Jul 30, 2024
e2bee66
more unused usings
trishorts Jul 30, 2024
068d541
close spectrum library connection
trishorts Jul 30, 2024
493f50b
added decoy sanitizing to MetaMorpheus task. Not sure why tests are b…
Alexander-Sol Aug 2, 2024
8a4492a
idk
Alexander-Sol Aug 2, 2024
13ff845
Merge branch 'master' into DecoyHomology3
trishorts Aug 5, 2024
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6 changes: 3 additions & 3 deletions MetaMorpheus/Bootstrapper/Bootstrapper.wixproj
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@@ -1,12 +1,12 @@
<Project Sdk="WixToolset.Sdk/4.0.0-rc.2">
<Project Sdk="WixToolset.Sdk/5.0.1">
<PropertyGroup>
<OutputName>MetaMorpheusInstaller</OutputName>
<OutputType>Bundle</OutputType>
<Platforms>x64;ARM64</Platforms>
</PropertyGroup>
<ItemGroup>
<PackageReference Include="WixToolset.Util.wixext" Version="4.0.0-rc.2" />
<PackageReference Include="WixToolset.Bal.wixext" Version="4.0.0-rc.2" />
<PackageReference Include="WixToolset.Util.wixext" Version="5.0.1" />
<PackageReference Include="WixToolset.Bal.wixext" Version="5.0.1" />
</ItemGroup>
<ItemGroup>
<ProjectReference Include="..\MetaMorpheusSetup\MetaMorpheusSetup.wixproj">
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12 changes: 6 additions & 6 deletions MetaMorpheus/CMD/CMD.csproj
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Expand Up @@ -2,7 +2,7 @@

<PropertyGroup>
<OutputType>Exe</OutputType>
<TargetFramework>net6.0</TargetFramework>
<TargetFramework>net8.0</TargetFramework>
<ApplicationManifest>app1.manifest</ApplicationManifest>
<Configurations>Debug;Release</Configurations>
<DebugType>full</DebugType>
Expand All @@ -19,12 +19,12 @@
</PropertyGroup>

<ItemGroup>
<PackageReference Include="CommandLineParser" Version="2.7.82" />
<PackageReference Include="Microsoft.ML" Version="2.0.0" />
<PackageReference Include="Microsoft.ML.CpuMath" Version="2.0.0" />
<PackageReference Include="Microsoft.ML.FastTree" Version="2.0.0" />
<PackageReference Include="CommandLineParser" Version="2.9.1" />
<PackageReference Include="Microsoft.ML" Version="3.0.1" />
<PackageReference Include="Microsoft.ML.CpuMath" Version="3.0.1" />
<PackageReference Include="Microsoft.ML.FastTree" Version="3.0.1" />
<PackageReference Include="Microsoft.NETCore.App" Version="2.2.8" />
<PackageReference Include="mzLib" Version="1.0.549" />
<PackageReference Include="mzLib" Version="5.1.547" />
<PackageReference Include="Nett" Version="0.15.0" />
</ItemGroup>

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14 changes: 7 additions & 7 deletions MetaMorpheus/EngineLayer/EngineLayer.csproj
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@@ -1,7 +1,7 @@
<Project Sdk="Microsoft.NET.Sdk">

<PropertyGroup>
<TargetFramework>net6.0</TargetFramework>
<TargetFramework>net8.0</TargetFramework>
<Configurations>Debug;Release</Configurations>
<Version>1.0.0.0</Version>
<DebugType>full</DebugType>
Expand All @@ -17,15 +17,15 @@
</PropertyGroup>

<ItemGroup>
<PackageReference Include="Microsoft.ML" Version="2.0.0" />
<PackageReference Include="Microsoft.ML.CpuMath" Version="2.0.0" />
<PackageReference Include="Microsoft.ML.FastTree" Version="2.0.0" />
<PackageReference Include="Microsoft.ML" Version="3.0.1" />
<PackageReference Include="Microsoft.ML.CpuMath" Version="3.0.1" />
<PackageReference Include="Microsoft.ML.FastTree" Version="3.0.1" />
<PackageReference Include="Microsoft.NETCore.App" Version="2.2.8" />
<PackageReference Include="mzLib" Version="1.0.549" />
<PackageReference Include="mzLib" Version="5.1.547" />
<PackageReference Include="NETStandard.Library" Version="2.0.3" />
<PackageReference Include="Nett" Version="0.15.0" />
<PackageReference Include="Newtonsoft.Json" Version="13.0.1" />
<PackageReference Include="TopDownProteomics" Version="0.0.290" />
<PackageReference Include="Newtonsoft.Json" Version="13.0.3" />
<PackageReference Include="TopDownProteomics" Version="0.0.297" />
</ItemGroup>

<ItemGroup>
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31 changes: 15 additions & 16 deletions MetaMorpheus/GUI/GUI.csproj
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Expand Up @@ -2,7 +2,7 @@

<PropertyGroup>
<OutputType>WinExe</OutputType>
<TargetFramework>net6.0-windows</TargetFramework>
<TargetFramework>net8.0-windows</TargetFramework>
<UseWPF>true</UseWPF>
<GenerateAssemblyTitleAttribute>false</GenerateAssemblyTitleAttribute>
<GenerateAssemblyConfigurationAttribute>false</GenerateAssemblyConfigurationAttribute>
Expand Down Expand Up @@ -50,28 +50,27 @@
<ItemGroup>
<PackageReference Include="MarkdownSharp" Version="2.0.5" />
<PackageReference Include="MathNet.Numerics" Version="5.0.0" />
<PackageReference Include="MathNet.Numerics.MKL.Win" Version="2.5.0" />
<PackageReference Include="Microsoft.ML" Version="2.0.0" />
<PackageReference Include="Microsoft.ML.CpuMath" Version="2.0.0" />
<PackageReference Include="Microsoft.ML.FastTree" Version="2.0.0" />
<PackageReference Include="Microsoft.ML" Version="3.0.1" />
<PackageReference Include="Microsoft.ML.CpuMath" Version="3.0.1" />
<PackageReference Include="Microsoft.ML.FastTree" Version="3.0.1" />
<PackageReference Include="Microsoft.NETCore.App" Version="2.2.8" />
<PackageReference Include="mzLib" Version="1.0.549" />
<PackageReference Include="mzLib" Version="5.1.547" />
<PackageReference Include="Nett" Version="0.15.0" />
<PackageReference Include="Newtonsoft.Json" Version="13.0.1" />
<PackageReference Include="Newtonsoft.Json" Version="13.0.3" />
<PackageReference Include="OxyPlot.Core" Version="2.0.0" />
<PackageReference Include="OxyPlot.Wpf" Version="2.0.0" />
<PackageReference Include="SharpLearning.CrossValidation" Version="0.26.9" />
<PackageReference Include="SharpLearning.GradientBoost" Version="0.26.9" />
<PackageReference Include="SharpLearning.Metrics" Version="0.26.9" />
<PackageReference Include="SharpLearning.CrossValidation" Version="0.31.8" />
<PackageReference Include="SharpLearning.GradientBoost" Version="0.31.8" />
<PackageReference Include="SharpLearning.Metrics" Version="0.31.8" />
<PackageReference Include="System.Buffers" Version="4.5.1" />
<PackageReference Include="System.CodeDom" Version="5.0.0" />
<PackageReference Include="System.Collections.Immutable" Version="5.0.0" />
<PackageReference Include="System.Drawing.Common" Version="5.0.3" />
<PackageReference Include="System.Memory" Version="4.5.4" />
<PackageReference Include="System.CodeDom" Version="8.0.0" />
<PackageReference Include="System.Collections.Immutable" Version="8.0.0" />
<PackageReference Include="System.Drawing.Common" Version="8.0.7" />
<PackageReference Include="System.Memory" Version="4.5.5" />
<PackageReference Include="System.Numerics.Vectors" Version="4.5.0" />
<PackageReference Include="System.Reflection.Emit.Lightweight" Version="4.7.0" />
<PackageReference Include="System.Runtime.CompilerServices.Unsafe" Version="5.0.0" />
<PackageReference Include="System.Threading.Tasks.Dataflow" Version="5.0.0" />
<PackageReference Include="System.Runtime.CompilerServices.Unsafe" Version="6.0.0" />
<PackageReference Include="System.Threading.Tasks.Dataflow" Version="8.0.1" />
<PackageReference Include="System.ValueTuple" Version="4.5.0" />
</ItemGroup>

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9 changes: 5 additions & 4 deletions MetaMorpheus/GuiFunctions/GuiFunctions.csproj
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@@ -1,7 +1,7 @@
<Project Sdk="Microsoft.NET.Sdk">

<PropertyGroup>
<TargetFramework>net6.0-windows</TargetFramework>
<TargetFramework>net8.0-windows</TargetFramework>
<Configurations>Debug;Release</Configurations>
<DebugType>full</DebugType>
<DebugSymbols>true</DebugSymbols>
Expand All @@ -13,10 +13,11 @@
</PropertyGroup>

<ItemGroup>
<PackageReference Include="itext7" Version="7.1.13" />
<PackageReference Include="mzLib" Version="1.0.549" />
<PackageReference Include="itext7" Version="8.0.5" />
<PackageReference Include="itext7.bouncy-castle-adapter" Version="8.0.5" />
<PackageReference Include="mzLib" Version="5.1.547" />
<PackageReference Include="OxyPlot.Wpf" Version="2.0.0" />
<PackageReference Include="Svg" Version="3.4.3" />
<PackageReference Include="Svg" Version="3.4.7" />
</ItemGroup>

<ItemGroup>
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5 changes: 0 additions & 5 deletions MetaMorpheus/GuiFunctions/MetaDraw/MetaDrawLogic.cs
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@@ -1,7 +1,4 @@
using EngineLayer;
using IO.Mgf;
using IO.MzML;
using IO.ThermoRawFileReader;
using iText.IO.Image;
using iText.Kernel.Pdf;
using MassSpectrometry;
Expand All @@ -20,8 +17,6 @@
using System.Windows.Media.Imaging;
using System.Windows.Shapes;
using Easy.Common.Extensions;
using EngineLayer.CrosslinkSearch;
using Org.BouncyCastle.Asn1.X509.Qualified;
using Readers;
using System.Threading;
using Omics.Fragmentation;
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7 changes: 0 additions & 7 deletions MetaMorpheus/GuiFunctions/MetaDraw/SpectrumMatch/SpectrumMatchPlot.cs
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Expand Up @@ -4,27 +4,20 @@
using System.Globalization;
using System.IO;
using System.Linq;
using System.Reflection;
using System.Text;
using System.Windows;
using System.Windows.Media;
using System.Windows.Media.Imaging;
using Chemistry;
using Easy.Common.Extensions;
using EngineLayer;
using iText.IO.Image;
using iText.Kernel.Pdf;
using iText.Layout;
using MassSpectrometry;
using MassSpectrometry.MzSpectra;
using mzPlot;
using Omics.Fragmentation;
using Omics.SpectrumMatch;
using OxyPlot;
using OxyPlot.Annotations;
using OxyPlot.Axes;
using OxyPlot.Series;
using Canvas = System.Windows.Controls.Canvas;
using FontWeights = OxyPlot.FontWeights;
using HorizontalAlignment = OxyPlot.HorizontalAlignment;
using VerticalAlignment = OxyPlot.VerticalAlignment;
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8 changes: 4 additions & 4 deletions MetaMorpheus/MetaMorpheusSetup/MetaMorpheusSetup.wixproj
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@@ -1,5 +1,5 @@
<Project>
<Import Project="Sdk.props" Sdk="WixToolset.Sdk" Version="4.0.0-rc.2" />
<Import Project="Sdk.props" Sdk="WixToolset.Sdk" Version="5.0.1" />
<PropertyGroup>
<Platform Condition=" '$(Platform)' == '' ">x64</Platform>
<OutputName>MetaMorpheusInstaller</OutputName>
Expand Down Expand Up @@ -53,10 +53,10 @@
</ProjectReference>
</ItemGroup>
<ItemGroup>
<PackageReference Include="WixToolset.Util.wixext" Version="4.0.0-rc.2" />
<PackageReference Include="WixToolset.UI.wixext" Version="4.0.0-rc.2" />
<PackageReference Include="WixToolset.Util.wixext" Version="5.0.1" />
<PackageReference Include="WixToolset.UI.wixext" Version="5.0.1" />
</ItemGroup>
<Import Project="Sdk.targets" Sdk="WixToolset.Sdk" Version="4.0.0-rc.2" />
<Import Project="Sdk.targets" Sdk="WixToolset.Sdk" Version="5.0.1" />
<PropertyGroup>
<PreBuildEvent />
</PropertyGroup>
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19 changes: 0 additions & 19 deletions MetaMorpheus/MetaMorpheusSetup/Product.wxs
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Expand Up @@ -24,7 +24,6 @@
<ComponentGroupRef Id="LinuxNativeMathComponents" />
<ComponentGroupRef Id="OsxNativeMathComponents" />
<ComponentGroupRef Id="WinNativeMathComponents" />
<ComponentGroupRef Id="MathNumerics_x64" />
<!--ComponentRef creates a reference to a Component element in another Fragment-->
<ComponentRef Id="MetaMorpheusProgramMenuFolderComponent" />

Expand Down Expand Up @@ -331,15 +330,6 @@
<Component Id="src_OpenMcdf.Extensions.dll" Guid="69004206-94FD-4342-A98D-70560B41C7B3">
<File Id="src_OpenMcdf.Extensions.dll" Name="OpenMcdf.Extensions.dll" Source="$(var.GUI_TargetDir)OpenMcdf.Extensions.dll" />
</Component>
<Component Id="src_Common.Logging.Core.dll" Guid="894B4A68-17E7-48A5-B2C6-74C33CD08979">
<File Id="src_Common.Logging.Core.dll" Name="Common.Logging.Core.dll" Source="$(var.GUI_TargetDir)Common.Logging.Core.dll" />
</Component>
<Component Id="src_Common.Logging.dll" Guid="B543DE60-4AE9-4C43-88A7-1B1F752D7171">
<File Id="src_Common.Logging.dll" Name="Common.Logging.dll" Source="$(var.GUI_TargetDir)Common.Logging.dll" />
</Component>
<Component Id="src_BouncyCastle.Crypto.dll" Guid="54F72A71-C672-4655-95AA-4D32C9983A7D">
<File Id="src_BouncyCastle.Crypto.dll" Name="BouncyCastle.Crypto.dll" Source="$(var.GUI_TargetDir)BouncyCastle.Crypto.dll" />
</Component>
<Component Id="src_Microsoft.DotNet.PlatformAbstractions.dll" Guid="F42DEDAA-6D88-4D5B-AB51-C472617F2C5F">
<File Id="src_Microsoft.DotNet.PlatformAbstractions.dll" Name="Microsoft.DotNet.PlatformAbstractions.dll" Source="$(var.GUI_TargetDir)Microsoft.DotNet.PlatformAbstractions.dll" />
</Component>
Expand Down Expand Up @@ -412,15 +402,6 @@
</Component>
</ComponentGroup>

<!--Other x64 Components-->
<ComponentGroup Id="MathNumerics_x64" Directory="MathNumericsFolder_x64">
<Component Id="src_libiomp5md.dll" Guid="CB28608B-0F60-4002-B0E3-F8A151DCD871">
<File Id="src_libiomp5md.dll" Name="libiomp5md.dll" Source="$(var.GUI_TargetDir)x64\libiomp5md.dll" />
</Component>
<Component Id="srcMathNet.Numerics.MKL.dll" Guid="9384C245-B63C-48EF-B5DA-8AB2C04A6B27">
<File Id="src_MathNet.Numerics.MKL.dll" Name="MathNet.Numerics.MKL.dll" Source="$(var.GUI_TargetDir)x64\MathNet.Numerics.MKL.dll" />
</Component>
</ComponentGroup>
</Fragment>

<!--Build the App Mods folder-->
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36 changes: 36 additions & 0 deletions MetaMorpheus/TaskLayer/MetaMorpheusTask.cs
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Expand Up @@ -621,6 +621,42 @@ protected List<Protein> LoadProteins(string taskId, List<DbForTask> dbFilenameLi
{
Warn("Warning: " + emptyProteinEntries + " empty protein entries ignored");
}

Status("Done loading proteins", new List<string> { taskId });

if (!proteinList.Any(p => p.IsDecoy))
{
return proteinList;
}

// Sanitize the decoys

HashSet<string> targetPeptideSequences = new();
foreach(var protein in proteinList.Where(p => !p.IsDecoy))
{
// When thinking about decoy collisions, we can ignore modifications
foreach(var peptide in protein.Digest(commonParameters.DigestionParams, new List<Modification>(), new List<Modification>()))
{
targetPeptideSequences.Add(peptide.BaseSequence);
}
}
// Now, we iterate through the decoys and scramble the sequences that correspond to target peptides
for(int i = 0; i < proteinList.Count; i++)
{
if(proteinList[i].IsDecoy)
{
var peptidesToReplace = proteinList[i]
.Digest(commonParameters.DigestionParams, new List<Modification>(), new List<Modification>())
.Select(p => p.BaseSequence)
.Where(targetPeptideSequences.Contains)
.ToList();
if(peptidesToReplace.Any())
{
proteinList[i] = Protein.ScrambleDecoyProteinSequence(proteinList[i], commonParameters.DigestionParams, forbiddenSequences: targetPeptideSequences, peptidesToReplace);
}
}
}

return proteinList;
}

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12 changes: 6 additions & 6 deletions MetaMorpheus/TaskLayer/TaskLayer.csproj
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@@ -1,7 +1,7 @@
<Project Sdk="Microsoft.NET.Sdk">

<PropertyGroup>
<TargetFramework>net6.0</TargetFramework>
<TargetFramework>net8.0</TargetFramework>
<Configurations>Debug;Release</Configurations>
<DebugType>full</DebugType>
<DebugSymbols>true</DebugSymbols>
Expand All @@ -17,12 +17,12 @@

<ItemGroup>
<PackageReference Include="MathNet.Numerics" Version="5.0.0" />
<PackageReference Include="Microsoft.ML" Version="2.0.0" />
<PackageReference Include="Microsoft.ML.CpuMath" Version="2.0.0" />
<PackageReference Include="Microsoft.ML.FastTree" Version="2.0.0" />
<PackageReference Include="Microsoft.ML" Version="3.0.1" />
<PackageReference Include="Microsoft.ML.CpuMath" Version="3.0.1" />
<PackageReference Include="Microsoft.ML.FastTree" Version="3.0.1" />
<PackageReference Include="Microsoft.NETCore.App" Version="2.2.8" />
<PackageReference Include="mzLib" Version="1.0.549" />
<PackageReference Include="NetSerializer" Version="4.1.1" />
<PackageReference Include="mzLib" Version="5.1.547" />
<PackageReference Include="NetSerializer" Version="4.1.2" />
<PackageReference Include="Nett" Version="0.15.0" />
</ItemGroup>

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2 changes: 1 addition & 1 deletion MetaMorpheus/Test/AddCompIonsTest.cs
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Expand Up @@ -5,7 +5,7 @@
using EngineLayer.ModernSearch;
using MassSpectrometry;
using MzLibUtil;
using NUnit.Framework;
using NUnit.Framework; using Assert = NUnit.Framework.Legacy.ClassicAssert;
using Proteomics;
using Omics.Fragmentation;
using Proteomics.ProteolyticDigestion;
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2 changes: 1 addition & 1 deletion MetaMorpheus/Test/AmbiguityTest.cs
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Expand Up @@ -2,7 +2,7 @@
using EngineLayer;
using EngineLayer.ClassicSearch;
using MzLibUtil;
using NUnit.Framework;
using NUnit.Framework; using Assert = NUnit.Framework.Legacy.ClassicAssert;
using Proteomics;
using Omics.Fragmentation;
using Proteomics.ProteolyticDigestion;
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2 changes: 1 addition & 1 deletion MetaMorpheus/Test/AnalysisEngineTest.cs
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Expand Up @@ -3,7 +3,7 @@
using EngineLayer.HistogramAnalysis;
using MassSpectrometry;
using MzLibUtil;
using NUnit.Framework;
using NUnit.Framework; using Assert = NUnit.Framework.Legacy.ClassicAssert;
using Proteomics;
using Omics.Fragmentation;
using Proteomics.ProteolyticDigestion;
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2 changes: 1 addition & 1 deletion MetaMorpheus/Test/AveragingGuiComponentsTest.cs
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Expand Up @@ -5,7 +5,7 @@
using System.Text;
using System.Threading.Tasks;
using GuiFunctions;
using NUnit.Framework;
using NUnit.Framework; using Assert = NUnit.Framework.Legacy.ClassicAssert;
using SpectralAveraging;

namespace Test
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2 changes: 1 addition & 1 deletion MetaMorpheus/Test/AveragingTests.cs
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Expand Up @@ -7,7 +7,7 @@
using FlashLFQ;
using GuiFunctions;
using MassSpectrometry;
using NUnit.Framework;
using NUnit.Framework; using Assert = NUnit.Framework.Legacy.ClassicAssert;
using Readers;
using SpectralAveraging;
using TaskLayer;
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2 changes: 1 addition & 1 deletion MetaMorpheus/Test/BinGenerationTest.cs
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@@ -1,6 +1,6 @@
using EngineLayer;
using MassSpectrometry;
using NUnit.Framework;
using NUnit.Framework; using Assert = NUnit.Framework.Legacy.ClassicAssert;
using Proteomics;
using Proteomics.ProteolyticDigestion;
using System;
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2 changes: 1 addition & 1 deletion MetaMorpheus/Test/CalibrationTests.cs
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Expand Up @@ -3,7 +3,7 @@
using EngineLayer.Calibration;
using FlashLFQ;
using MassSpectrometry;
using NUnit.Framework;
using NUnit.Framework; using Assert = NUnit.Framework.Legacy.ClassicAssert;
using System;
using System.Collections.Generic;
using System.ComponentModel;
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2 changes: 1 addition & 1 deletion MetaMorpheus/Test/CoIsolationTests.cs
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Expand Up @@ -3,7 +3,7 @@
using EngineLayer.ClassicSearch;
using MassSpectrometry;
using MzLibUtil;
using NUnit.Framework;
using NUnit.Framework; using Assert = NUnit.Framework.Legacy.ClassicAssert;
using Proteomics;
using Omics.Fragmentation;
using Proteomics.ProteolyticDigestion;
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