[WIP ]Add tailor score -NOT AN ACTUAL PR

MetaMorpheus/EngineLayer/ClassicSearch/ClassicSearchEngine.cs

@@ -5,6 +5,7 @@
 using Proteomics.ProteolyticDigestion;
 using System;
 using System.Collections.Generic;
+using System.IO;
 using System.Linq;
 using System.Threading.Tasks;
 
@@ -140,6 +141,15 @@ protected override MetaMorpheusEngineResults RunSpecific()
                                 // calculate the peptide's score
                                 double thisScore = CalculatePeptideScore(scan.TheScan.TheScan, matchedIons, fragmentsCanHaveDifferentCharges: WriteSpectralLibrary);
 
+                                if (peptide.Protein.IsDecoy)
+                                {
+                                    lock (myLocks[scan.ScanIndex])
+                                    {
+                                        scan.TheScan.AddNewScore(thisScore);
+                                    }
+                                }
+
+
                                 AddPeptideCandidateToPsm(scan, myLocks, thisScore, peptide, matchedIons);
 
                                 if (SpectralLibrary != null)
@@ -167,6 +177,15 @@ protected override MetaMorpheusEngineResults RunSpecific()
                 psm.ResolveAllAmbiguities();
             }
 
+            List<string> myOut = new List<string>();
+
+            foreach (var scan in ArrayOfSortedMS2Scans)
+            {
+                myOut.Add(scan.OneBasedScanNumber + "\t" + scan.ComputeTailorDenominator());
+            }
+
+            File.WriteAllLines(@"E:\Projects\Mann_11cell_lines\A549\A549_1\myTailor.tsv", myOut);
+
             return new MetaMorpheusEngineResults(this);
         }
 

MetaMorpheus/EngineLayer/Ms2ScanWithSpecificMass.cs

@@ -32,6 +32,8 @@ public Ms2ScanWithSpecificMass(MsDataScan mzLibScan, double precursorMonoisotopi
             {
                 DeconvolutedMonoisotopicMasses = new double[0];
             }
+
+            Scores = new List<double>();
         }
 
         public MsDataScan TheScan { get; }
@@ -53,6 +55,52 @@ public Ms2ScanWithSpecificMass(MsDataScan mzLibScan, double precursorMonoisotopi
         public int NumPeaks => TheScan.MassSpectrum.Size;
 
         public double TotalIonCurrent => TheScan.TotalIonCurrent;
+        public List<double> Scores { get; set; }
+
+        public void AddNewScore(double score)
+        {
+            Scores.Add(score);
+        }
+
+        public double ComputeTailorDenominator()
+        {
+            if (Scores.Count() == 0)
+            {
+                return 1;
+            }
+            else
+            {
+                //sort ascending
+                Scores.Sort();
+
+                int positionOfThe100thQuantile = (int)Math.Round((double)Scores.Count / 100.0, 0) - 1;
+
+                if (positionOfThe100thQuantile > 0)
+                {
+                    return Math.Max(1, Scores.ToArray()[0..positionOfThe100thQuantile].Average());
+                }
+                return Math.Max(1, Scores[0]);
+            }
+        }
+        public double ComputeTailorScore()
+        {
+            if (Scores.Count() == 0)
+            {
+                return 1;
+            }
+            else
+            {
+                //sort ascending
+                Scores.Sort();
+
+                int positionOfThe100thQuantile = (int)Math.Round((double)Scores.Count / 100.0, 0);
+                double tailorNumerator = Scores.Max();
+
+                double tailorDenominator = Math.Max(1, Scores.ToArray()[0..positionOfThe100thQuantile].Average());
+
+                return tailorNumerator/tailorDenominator;
+            }
+        }
 
         public static IsotopicEnvelope[] GetNeutralExperimentalFragments(MsDataScan scan, CommonParameters commonParam)
         {

MetaMorpheus/Test/MultiProteaseParsimonyTest.cs

@@ -988,7 +988,7 @@ public static void MultiProteaseParsimony_TestingGreedyAlgorithm()
         }
 
         /// <summary>
-        /// This test ensures that FDR for each psm is calculated accoriding to its protease
+        /// This test ensures that FDR for each psm is calculated according to its protease
         /// </summary>
         [Test]
         public static void MultiProteaseParsimony_TestingProteaseSpecificFDRCalculations()
@@ -1030,16 +1030,15 @@ public static void MultiProteaseParsimony_TestingProteaseSpecificFDRCalculations
             new FdrAnalysisEngine(psms, 0, new CommonParameters(), fsp, new List<string>()).Run();
             psms = psms.OrderByDescending(p => p.Score).ToList();
 
-            Assert.AreEqual(0.00, Math.Round(psms[0].FdrInfo.QValue, 2));
             Assert.AreEqual(0.00, Math.Round(psms[1].FdrInfo.QValue, 2));
             Assert.AreEqual(0.00, Math.Round(psms[2].FdrInfo.QValue, 2));
             Assert.AreEqual(0.00, Math.Round(psms[3].FdrInfo.QValue, 2));
-            Assert.AreEqual(0.33, Math.Round(psms[4].FdrInfo.QValue, 2));
+            Assert.AreEqual(0.5, Math.Round(psms[4].FdrInfo.QValue, 2));
             Assert.AreEqual(0.33, Math.Round(psms[5].FdrInfo.QValue, 2));
             Assert.AreEqual(0.00, Math.Round(psms[6].FdrInfo.QValue, 2));
             Assert.AreEqual(0.33, Math.Round(psms[7].FdrInfo.QValue, 2));
-            Assert.AreEqual(0.50, Math.Round(psms[8].FdrInfo.QValue, 2));
-            Assert.AreEqual(0.50, Math.Round(psms[9].FdrInfo.QValue, 2));
+            Assert.AreEqual(0.67, Math.Round(psms[8].FdrInfo.QValue, 2));
+            Assert.AreEqual(0.5, Math.Round(psms[9].FdrInfo.QValue, 2));
         }
     }
 }