From 2a3eaaf325a410cd40553ff5ad3eba2434cdde44 Mon Sep 17 00:00:00 2001
From: RayMSMS <150720362+RayMSMS@users.noreply.github.com>
Date: Wed, 7 May 2025 12:55:48 -0500
Subject: [PATCH] Add the  peak filter

---
 mzLib/FlashLFQ/FlashLfqEngine.cs       | 4 +++-
 mzLib/FlashLFQ/FlashLfqParameters.cs   | 2 ++
 mzLib/FlashLFQ/IsoTracker/XICGroups.cs | 7 ++++---
 3 files changed, 9 insertions(+), 4 deletions(-)

diff --git a/mzLib/FlashLFQ/FlashLfqEngine.cs b/mzLib/FlashLFQ/FlashLfqEngine.cs
index ebbe66abc..1546db04c 100644
--- a/mzLib/FlashLFQ/FlashLfqEngine.cs
+++ b/mzLib/FlashLFQ/FlashLfqEngine.cs
@@ -125,6 +125,7 @@ public FlashLfqEngine(
 
             // IsoTracker settings
             bool isoTracker = false,
+            double acceptablePeakWidth = 0.4,
 
             // MBR settings
             bool matchBetweenRuns = false,
@@ -157,6 +158,7 @@ public FlashLfqEngine(
                     MaxThreads = maxThreads,
                     Normalize = normalize,
                     IsoTracker = isoTracker,
+                    AcceptablePeakWidth = acceptablePeakWidth,
                     MatchBetweenRuns = matchBetweenRuns,
                     MaxMbrRtWindow = maxMbrWindow,
                     MbrPpmTolerance = matchBetweenRunsPpmTolerance,
@@ -1892,7 +1894,7 @@ private void QuantifyIsobaricPeaks()
                             foreach (var peak in xICGroups.SharedPeaks)
                             {
                                 double peakWindow = peak.Width;
-                                if (peakWindow > 0.001) //make sure we have enough length of the window (0.001 min) for peak searching
+                                if (peakWindow > FlashParams.AcceptablePeakWidth) //make sure we have enough length of the window (default is 0.4 min) for peak searching
                                 {
                                     List<ChromatographicPeak> chromPeaksInSharedPeak = new List<ChromatographicPeak>();
                                     CollectChromPeakInRuns(peak, chromPeaksInSharedPeak, xICGroups);
diff --git a/mzLib/FlashLFQ/FlashLfqParameters.cs b/mzLib/FlashLFQ/FlashLfqParameters.cs
index 4a79fb9ec..bbc17d53c 100644
--- a/mzLib/FlashLFQ/FlashLfqParameters.cs
+++ b/mzLib/FlashLFQ/FlashLfqParameters.cs
@@ -23,6 +23,7 @@ public FlashLfqParameters()
 
             // IsoTracker settings
             IsoTracker = false;
+            AcceptablePeakWidth = 0.4; // The acceptable peak width for the isobaric peaks. This is used to determine the peak width of the isobaric peaks
 
             // MBR settings
             MatchBetweenRuns = false;
@@ -56,6 +57,7 @@ public FlashLfqParameters()
 
         //IsoTracker settings
         public bool IsoTracker { get; set; } //Searching parameter for the FlashLFQ engine
+        public double AcceptablePeakWidth { get; set; }
 
         // MBR settings
         public bool MatchBetweenRuns { get; set; }
diff --git a/mzLib/FlashLFQ/IsoTracker/XICGroups.cs b/mzLib/FlashLFQ/IsoTracker/XICGroups.cs
index f74a14520..de3c55da0 100644
--- a/mzLib/FlashLFQ/IsoTracker/XICGroups.cs
+++ b/mzLib/FlashLFQ/IsoTracker/XICGroups.cs
@@ -91,7 +91,7 @@ public void FindSharedExtrema(double count_threshold, double tolerance, double c
 
             SharedExtrema = group_min.Concat(group_max).ToList();
             SharedExtrema.Sort((p1, p2) => p1.RetentionTime.CompareTo(p2.RetentionTime)); // sort the shared extrema by the retention time
-            SharePeakTrimming();
+            ExtremaTrimming(); // Just rename the function to be more readable
 
 
         }
@@ -145,8 +145,8 @@ private List<Extremum> SortExtrema(List<Extremum> extremaList, double tolerance,
         /// <summary>
         /// Trim the shared extremas in the close time range. Ex. if the two minimums are close and the intensity is going up, remove the first one
         /// </summary>
-        /// <param name="cutOff"> The time range for trimming</param>
-        private void SharePeakTrimming(double cutOff = 0.3) 
+        /// <param name="cutOff"> The acceptable time for differentiate two extrema range for trimming</param>
+        private void ExtremaTrimming(double cutOff = 0.3) 
         {
             int removeIndex = 0;
             int count = SharedExtrema.Count();
@@ -244,6 +244,7 @@ public List<PeakRegion> BuildSharedPeaks(double windowLimit = 0.3)
             }
 
             // remove the peaks with the time window less than the window limit
+            // We already have a limit peak width for the peak region.
             sharedPeaks.RemoveAll(p => p.Width < windowLimit);
             return sharedPeaks;
         }