From 0d5c6914fe5f8bdddcbf18d7bf37eda2cf216eab Mon Sep 17 00:00:00 2001
From: "DESKTOP-382ETUR\\Hiroshi Tsugawa" <htsugawa@go.tuat.ac.jp>
Date: Sun, 8 Feb 2026 23:41:32 +0900
Subject: [PATCH] modified the source code to exclude duplicated metabolite
 info.

---
 .../Algorithm/Alignment/SpotAction.cs         | 10 ++---
 .../MsdialGcMsApi/Algorithm/Annotation.cs     | 41 ++++++++++++++++++-
 2 files changed, 45 insertions(+), 6 deletions(-)

diff --git a/src/MSDIAL5/MsdialCore/Algorithm/Alignment/SpotAction.cs b/src/MSDIAL5/MsdialCore/Algorithm/Alignment/SpotAction.cs
index 9b8ee3f03..b53ab3a2a 100644
--- a/src/MSDIAL5/MsdialCore/Algorithm/Alignment/SpotAction.cs
+++ b/src/MSDIAL5/MsdialCore/Algorithm/Alignment/SpotAction.cs
@@ -30,7 +30,7 @@ public MatchResultAnnotationDeduplicator(IMatchResultEvaluator<MsScanMatchResult
         }
 
         public void Process(IEnumerable<AlignmentSpotProperty> spots) {
-            var spotList = spots.Where(n => n.IsReferenceMatched(_evaluator)).OrderByDescending(spot => spot.MatchResults.Representative.LibraryID).ToList();
+            var spotList = spots.Where(n => n.IsReferenceMatched(_evaluator) && !n.Name.StartsWith("Putative")).OrderByDescending(spot => spot.MatchResults.Representative.LibraryID).ToList();
             var currentPeakId = 0;
             var currentLibraryId = spotList[currentPeakId].MatchResults.Representative.LibraryID;
 
@@ -56,7 +56,7 @@ public void Process(IEnumerable<AlignmentSpotProperty> spots) {
 
             // by InChIKey
             spotList = spots
-                       .Where(n => n.IsReferenceMatched(_evaluator))
+                       .Where(n => n.IsReferenceMatched(_evaluator) && !n.Name.StartsWith("Putative"))
                        .Where(n => !string.IsNullOrEmpty(n.MatchResults?.Representative?.InChIKey) && n.MatchResults.Representative.InChIKey.Length > 1)
                        .OrderByDescending(spot => spot.MatchResults.Representative.InChIKey)
                        .ToList();
@@ -83,7 +83,7 @@ public void Process(IEnumerable<AlignmentSpotProperty> spots) {
 
             // by Name
             spotList = spots
-                .Where(n => n.IsReferenceMatched(_evaluator))
+                .Where(n => n.IsReferenceMatched(_evaluator) && !n.Name.StartsWith("Putative"))
                 .Where(n => !n.MatchResults.Representative.Name.IsEmptyOrNull())
                 .OrderByDescending(spot => spot.MatchResults.Representative.Name)
                 .ToList();
@@ -110,8 +110,8 @@ public void Process(IEnumerable<AlignmentSpotProperty> spots) {
         }
 
         static void ChangeAnnotationToLowScore(AlignmentSpotProperty spot) {
-            spot.MatchResults.Representative.IsReferenceMatched = false;
-            spot.Name = "putative: " + spot.Name;
+            //spot.MatchResults.Representative.IsReferenceMatched = false;
+            spot.Name = "Putative: " + spot.Name;
         }
     }
 
diff --git a/src/MSDIAL5/MsdialGcMsApi/Algorithm/Annotation.cs b/src/MSDIAL5/MsdialGcMsApi/Algorithm/Annotation.cs
index 264876960..918ca0587 100644
--- a/src/MSDIAL5/MsdialGcMsApi/Algorithm/Annotation.cs
+++ b/src/MSDIAL5/MsdialGcMsApi/Algorithm/Annotation.cs
@@ -52,7 +52,7 @@ public AnnotatedMSDecResult[] MainProcess(IReadOnlyList<MSDecResult> ms1DecResul
 
                 var features = new AnnotatedMSDecResult[ms1DecResults.Count];
                 if (_parameter.OnlyReportTopHitInMspSearch) {
-                    var used = new HashSet<MoleculeMsReference>();
+                    var used = new HashSet<MoleculeMsReference>(new MoleculeMsReferenceEqualityComparer());
                     foreach (var (container, i) in containers.WithIndex().OrderByDescending(p => p.Item1.Representative.TotalScore)) {
                         if (container.Representative is MsScanMatchResult topHit && !topHit.IsUnknown) {
                             ms1DecResults[i].MspIDs.AddRange(containers[i].MatchResults.OrderByDescending(r => r.TotalScore).Select(r => r.LibraryID));
@@ -99,4 +99,43 @@ public AnnotatedMSDecResult[] MainProcess(IReadOnlyList<MSDecResult> ms1DecResul
             return ms1DecResults.Select(r => new AnnotatedMSDecResult(r, new MsScanMatchResultContainer())).ToArray();
         }
     }
+
+    public class MoleculeMsReferenceEqualityComparer : IEqualityComparer<MoleculeMsReference> {
+        public bool Equals(MoleculeMsReference x, MoleculeMsReference y) {
+            if (ReferenceEquals(x, y)) return true;
+            if (x is null || y is null) return false;
+
+            if (!string.IsNullOrEmpty(x.InChIKey) && !string.IsNullOrEmpty(y.InChIKey)) {
+                if (x.InChIKey == y.InChIKey) return true;
+            }
+
+            if (x.ScanID != 0 && y.ScanID != 0 && x.ScanID == y.ScanID) {
+                return true;
+            }
+
+            if (!string.IsNullOrEmpty(x.Name) && !string.IsNullOrEmpty(y.Name)) {
+                if (x.Name.ToLower() == y.Name.ToLower()) return true;
+            }
+
+            return false;
+        }
+
+        public int GetHashCode(MoleculeMsReference obj) {
+            if (obj is null) return 0;
+
+            if (!string.IsNullOrEmpty(obj.InChIKey)) {
+                return obj.InChIKey.GetHashCode();
+            }
+
+            if (obj.ScanID != 0) {
+                return obj.ScanID.GetHashCode();
+            }
+
+            if (!string.IsNullOrEmpty(obj.Name)) {
+                return obj.Name.ToLower().GetHashCode();
+            }
+
+            return 0;
+        }
+    }
 }