From 64113600faa638935abff8e9feea64fc14ed8a7c Mon Sep 17 00:00:00 2001
From: Alexander-Sol <41119316+Alexander-Sol@users.noreply.github.com>
Date: Mon, 18 Nov 2024 14:55:50 -0600
Subject: [PATCH] Fixed decoy order (#809)

---
 mzLib/Test/DatabaseTests/TestDatabaseLoaders.cs          | 5 ++---
 mzLib/UsefulProteomicsDatabases/DecoyProteinGenerator.cs | 2 ++
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/mzLib/Test/DatabaseTests/TestDatabaseLoaders.cs b/mzLib/Test/DatabaseTests/TestDatabaseLoaders.cs
index 8925661cb..776c5686d 100644
--- a/mzLib/Test/DatabaseTests/TestDatabaseLoaders.cs
+++ b/mzLib/Test/DatabaseTests/TestDatabaseLoaders.cs
@@ -110,9 +110,8 @@ public void LoadingIsReproducible(string fileName, DecoyType decoyType)
 
             // check are equivalent lists of proteins
             Assert.AreEqual(proteins1.Count, proteins2.Count);
-            // Because decoys are written in a parallel environment, there is no guarantee that the orders will be the same
-            CollectionAssert.AreEquivalent(proteins1.Select(p => p.Accession), proteins2.Select(p => p.Accession));
-            CollectionAssert.AreEquivalent(proteins1.Select(p => p.BaseSequence), proteins2.Select(p => p.BaseSequence));
+            // Because decoys are sorted before they are returned, the order should be identical
+            Assert.AreEqual(proteins1, proteins2);
         }
 
         [Test]
diff --git a/mzLib/UsefulProteomicsDatabases/DecoyProteinGenerator.cs b/mzLib/UsefulProteomicsDatabases/DecoyProteinGenerator.cs
index 67a442782..07a90b6f0 100644
--- a/mzLib/UsefulProteomicsDatabases/DecoyProteinGenerator.cs
+++ b/mzLib/UsefulProteomicsDatabases/DecoyProteinGenerator.cs
@@ -180,6 +180,7 @@ private static List<Protein> GenerateReverseDecoys(List<Protein> proteins, int m
 
                 lock (decoyProteins) { decoyProteins.Add(decoyProtein); }
             });
+            decoyProteins = decoyProteins.OrderBy(p => p.Accession).ToList();
             return decoyProteins;
         }
 
@@ -359,6 +360,7 @@ private static List<Protein> GenerateSlideDecoys(List<Protein> proteins, int max
                     protein.Name, protein.FullName, true, protein.IsContaminant, null, decoyVariationsSlide, null, protein.SampleNameForVariants, decoy_disulfides_slide, spliceSitesSlide, protein.DatabaseFilePath);
                 lock (decoyProteins) { decoyProteins.Add(decoyProteinSlide); }
             });
+            decoyProteins = decoyProteins.OrderBy(p => p.Accession).ToList();
             return decoyProteins;
         }