From 5186b827f9c6556eb5b4dc01d59a52bc9335ea2c Mon Sep 17 00:00:00 2001
From: trishorts <mshort@chem.wisc.edu>
Date: Tue, 15 Oct 2024 14:09:25 -0500
Subject: [PATCH] add override qValue threshold for unit testing

---
 .../EngineLayer/FdrAnalysis/FdrAnalysisEngine.cs       | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/MetaMorpheus/EngineLayer/FdrAnalysis/FdrAnalysisEngine.cs b/MetaMorpheus/EngineLayer/FdrAnalysis/FdrAnalysisEngine.cs
index c8a7cdcd9..576a61bb4 100644
--- a/MetaMorpheus/EngineLayer/FdrAnalysis/FdrAnalysisEngine.cs
+++ b/MetaMorpheus/EngineLayer/FdrAnalysis/FdrAnalysisEngine.cs
@@ -14,11 +14,12 @@ public class FdrAnalysisEngine : MetaMorpheusEngine
         private readonly string AnalysisType;
         private readonly string OutputFolder; // used for storing PEP training models  
         private readonly bool DoPEP;
+        private readonly bool QvalueThresholdOverride;
         private readonly int PsmCountThresholdForInvertedQvalue = 1000;
 
         public FdrAnalysisEngine(List<SpectralMatch> psms, int massDiffAcceptorNumNotches, CommonParameters commonParameters,
             List<(string fileName, CommonParameters fileSpecificParameters)> fileSpecificParameters, List<string> nestedIds, string analysisType = "PSM", 
-            bool doPEP = true, string outputFolder = null) : base(commonParameters, fileSpecificParameters, nestedIds)
+            bool doPEP = true, string outputFolder = null, bool qvalueThresholdOverride = false) : base(commonParameters, fileSpecificParameters, nestedIds)
         {
             AllPsms = psms.OrderByDescending(p => p).ToList();
             MassDiffAcceptorNumNotches = massDiffAcceptorNumNotches;
@@ -28,6 +29,7 @@ public FdrAnalysisEngine(List<SpectralMatch> psms, int massDiffAcceptorNumNotche
             if (AllPsms.Any())
                 AddPsmAndPeptideFdrInfoIfNotPresent();
             if (fileSpecificParameters == null) throw new ArgumentNullException("file specific parameters cannot be null");
+            QvalueThresholdOverride = qvalueThresholdOverride;
         }
 
         private void AddPsmAndPeptideFdrInfoIfNotPresent()
@@ -72,10 +74,10 @@ private void DoFalseDiscoveryRateAnalysis(FdrAnalysisResults myAnalysisResults)
                         .Select(b => b.FirstOrDefault())
                         .ToList();
 
-                if (psms.Count > PsmCountThresholdForInvertedQvalue & DoPEP)
+                if ((psms.Count > PsmCountThresholdForInvertedQvalue || QvalueThresholdOverride) & DoPEP)
                 {
                     CalculateQValue(psms, peptideLevelCalculation: false, pepCalculation: false);
-                    if (peptides.Count > PsmCountThresholdForInvertedQvalue)
+                    if (peptides.Count > PsmCountThresholdForInvertedQvalue || QvalueThresholdOverride)
                     {
                         CalculateQValue(peptides, peptideLevelCalculation: true, pepCalculation: false);
 
@@ -200,7 +202,7 @@ public void CalculateQValue(List<SpectralMatch> psms, bool peptideLevelCalculati
             }
             else
             {
-                if(psms.Count < PsmCountThresholdForInvertedQvalue)
+                if(psms.Count < PsmCountThresholdForInvertedQvalue || QvalueThresholdOverride)
                 {
 
                    QValueTraditional(psms, peptideLevelAnalysis: peptideLevelCalculation);