merged in master

nbollis · Sep 4, 2024 · f9030f9 · f9030f9
2 parents 0abcd9b + dd5e3b2
commit f9030f9
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diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -0,0 +1,37 @@
+# This workflow will build a .NET project
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-net
+
+name: Build
+
+on:
+  push:
+    branches: [ "master" ] 
+  pull_request:
+    branches: [ "master" ]
+
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+    name: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, windows-latest, macos-latest]
+        include: 
+          - os: ubuntu-latest
+            configuration: UbuntuMac
+          - os: macos-latest
+            configuration: UbuntuMac
+          - os: windows-latest
+            configuration: Release
+
+    steps:
+      - uses: actions/checkout@v4
+      - name: Setup .NET
+        uses: actions/setup-dotnet@v4
+        with:
+          dotnet-version: 8.0.204
+      - name: Restore dependencies
+        run: dotnet restore ./MetaMorpheus/MetaMorpheus.sln
+      - name: Build
+        run: dotnet build --no-restore ./MetaMorpheus/MetaMorpheus.sln --configuration ${{ matrix.configuration }}
diff --git a/MetaMorpheus/CMD/CMD.csproj b/MetaMorpheus/CMD/CMD.csproj
@@ -24,7 +24,7 @@
     <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="1.0.550" />
+    <PackageReference Include="mzLib" Version="1.0.551" />
     <PackageReference Include="Nett" Version="0.15.0" />
   </ItemGroup>
 

diff --git a/MetaMorpheus/EngineLayer/CommonParameters.cs b/MetaMorpheus/EngineLayer/CommonParameters.cs
@@ -163,7 +163,7 @@ public int DeconvolutionMaxAssumedChargeState
         /// This parameter determines which PSMs/Peptides will be used as postive training examples
         /// when training the GBDT model for PEP. 
         /// </summary>
-        public double QValueCutoffForPepCalculation { get; private set; }
+        public double QValueCutoffForPepCalculation { get; set; }
         public DigestionParams DigestionParams { get; private set; }
         public bool ReportAllAmbiguity { get; private set; }
         public int? NumberOfPeaksToKeepPerWindow { get; private set; }

diff --git a/MetaMorpheus/EngineLayer/EngineLayer.csproj b/MetaMorpheus/EngineLayer/EngineLayer.csproj
@@ -21,7 +21,7 @@
     <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="1.0.550" />
+    <PackageReference Include="mzLib" Version="1.0.551" />
     <PackageReference Include="NETStandard.Library" Version="2.0.3" />
     <PackageReference Include="Nett" Version="0.15.0" />
     <PackageReference Include="Newtonsoft.Json" Version="13.0.3" />

diff --git a/MetaMorpheus/EngineLayer/FdrAnalysis/FdrAnalysisEngine.cs b/MetaMorpheus/EngineLayer/FdrAnalysis/FdrAnalysisEngine.cs
@@ -1,4 +1,5 @@
-using System;
+using EngineLayer.CrosslinkSearch;
+using System;
 using System.Collections.Generic;
 using System.IO;
 using System.Linq;
@@ -275,18 +276,25 @@ public static void PepQValueInverted(List<SpectralMatch> psms, bool peptideLevel
 
         public void Compute_PEPValue(FdrAnalysisResults myAnalysisResults, List<SpectralMatch> psms)
         {
-            if (psms[0].DigestionParams.Protease.Name == "top-down")
+            string searchType;
+            // Currently, searches of mixed data (bottom-up + top-down) are not supported
+            // PEP will be calculated based on the search type of the first file/PSM in the list, which isn't ideal
+            // This will be addressed in a future release
+            switch(psms[0].DigestionParams.Protease.Name)
             {
-                myAnalysisResults.BinarySearchTreeMetrics = PEP_Analysis_Cross_Validation.ComputePEPValuesForAllPSMsGeneric(psms, "top-down", this.FileSpecificParameters, this.OutputFolder);
+               case "top-down":
+                    searchType = "top-down";
+                    break;
+                default:
+                    searchType = "standard";
+                    break;
             }
-            else if (psms[0].DigestionParams.Protease.Name == "crosslink")
+            if (psms[0] is CrosslinkSpectralMatch)
             {
-                myAnalysisResults.BinarySearchTreeMetrics = PEP_Analysis_Cross_Validation.ComputePEPValuesForAllPSMsGeneric(psms, "crosslink", this.FileSpecificParameters, this.OutputFolder);
-            }
-            else
-            {
-                myAnalysisResults.BinarySearchTreeMetrics = PEP_Analysis_Cross_Validation.ComputePEPValuesForAllPSMsGeneric(psms, "standard", this.FileSpecificParameters, this.OutputFolder);
+                searchType = "crosslink";
             }
+            myAnalysisResults.BinarySearchTreeMetrics = new PepAnalysisEngine(psms, searchType, FileSpecificParameters, OutputFolder).ComputePEPValuesForAllPSMs();
+
         }
 
         /// <summary>