isobaric quant engine and results

mzLib/IsobaricQuant/IsobaricQuant.csproj

@@ -0,0 +1,9 @@
+<Project Sdk="Microsoft.NET.Sdk">
+
+  <PropertyGroup>
+    <TargetFramework>net8.0</TargetFramework>
+    <ImplicitUsings>enable</ImplicitUsings>
+    <Nullable>enable</Nullable>
+  </PropertyGroup>
+
+</Project>

mzLib/IsobaricQuant/IsobaricQuantResults.cs

@@ -0,0 +1,19 @@
+using System;
+using System.Collections.Generic;
+using System.Linq;
+using System.Text;
+using System.Threading.Tasks;
+
+namespace IsobaricQuant
+{
+    internal class IsobaricQuantResults
+    {
+        public readonly List<TmtFileInfo> TmtSpectraFiles;
+
+
+        public IsobaricQuantResults(List<TmtFileInfo> tmtSpectraFiles)
+        {
+            TmtSpectraFiles = tmtSpectraFiles;
+        }
+    }
+}

mzLib/IsobaricQuant/TmtFileInfo.cs

@@ -0,0 +1,45 @@
+using System;
+using System.Collections.Generic;
+using System.Linq;
+using System.Text;
+using System.Threading.Tasks;
+
+namespace IsobaricQuant
+{
+    internal class TmtFileInfo
+    {
+        public TmtFileInfo(string fullFilePathWithExtension, string plex, int fraction, int technicalReplicate, IReadOnlyList<TmtPlexAnnotation> annotations)
+        {
+            FullFilePathWithExtension = fullFilePathWithExtension;
+            Plex = plex ?? string.Empty;
+            Fraction = fraction;
+            TechnicalReplicate = technicalReplicate;
+            Annotations = annotations ?? Array.Empty<TmtPlexAnnotation>();
+        }
+
+        public string FullFilePathWithExtension { get; }
+        public string Plex { get; }
+        public int Fraction { get; }             // 1-based
+        public int TechnicalReplicate { get; }   // 1-based
+        public IReadOnlyList<TmtPlexAnnotation> Annotations { get; } // All tags for this file's plex
+        public override bool Equals(object obj)
+        {
+            if (base.Equals(obj))
+            {
+                return ((TmtFileInfo)obj).FullFilePathWithExtension.Equals(FullFilePathWithExtension);
+            }
+
+            return false;
+        }
+
+        public override int GetHashCode()
+        {
+            return FullFilePathWithExtension.GetHashCode();
+        }
+
+        public override string ToString()
+        {
+            return Path.GetFileName(FullFilePathWithExtension);
+        }
+    }
+}

mzLib/IsobaricQuant/TmtPlexAnnotation.cs

@@ -0,0 +1,16 @@
+using System;
+using System.Collections.Generic;
+using System.Linq;
+using System.Text;
+using System.Threading.Tasks;
+
+namespace IsobaricQuant
+{
+    internal class TmtPlexAnnotation
+    {
+        public string Tag { get; set; } = "";
+        public string SampleName { get; set; } = "";
+        public string Condition { get; set; } = "";
+        public int BiologicalReplicate { get; set; }
+    }
+}

mzLib/Test/IsobaricQuant.cs

@@ -0,0 +1,173 @@
+using IsobaricQuant;
+using NUnit.Framework;
+using Readers;
+using System;
+using System.Collections.Concurrent;
+using System.Collections.Generic;
+using System.IO;
+using System.Linq;
+using System.Text;
+using System.Threading.Tasks;
+
+namespace Test
+{
+    [TestFixture]
+    internal class IsobaricQuant
+    {
+        [Test]
+        public void Ctor_WithValidInput()
+        {
+            var input = new List<(int peptideFullSequenceHash, int[] reporterIntensities)>
+            {
+                (2, new[]{49,56,30}),
+                (3, new[]{86,45,97}),
+                (6, new[]{61,59,44}),
+                (1, new[]{35,32,86}),
+                (2, new[]{35,31,13}),
+                (6, new[]{49,74,18}),
+                (4, new[]{87,9,23}),
+                (4, new[]{12,63,63}),
+                (5, new[]{0,84,96}),
+                (3, new[]{54,53,54}),
+                (1, new[]{24,11,9}),
+                (5, new[]{35,25,77})
+            };
+            var inputList = new List<List<(int peptideFullSequenceHash, int[] reporterIntensities)>> { input };
+            IsobaricQuantEngine ibq = new IsobaricQuantEngine(inputList);
+            var o1 = ibq.Process(aggregateType: IsobaricQuantEngine.AggregateType.SumTopN);
+            var o2 = ibq.Process(aggregateType: IsobaricQuantEngine.AggregateType.Max);
+            var o3 = ibq.Process(aggregateType: IsobaricQuantEngine.AggregateType.Median);
+            var o4 = ibq.Process(aggregateType: IsobaricQuantEngine.AggregateType.SumTopN, topN: 2);
+            var o5 = ibq.Process(aggregateType: IsobaricQuantEngine.AggregateType.SumTopN, lowFraction: 0.2);
+            var o6 = ibq.Process(aggregateType: IsobaricQuantEngine.AggregateType.SumTopN, normalize: false);
+            var o7 = ibq.Process(aggregateType: IsobaricQuantEngine.AggregateType.SumTopN, topN: 2, referenceChannel: 3);
+            var input2 = new List<(int peptideFullSequenceHash, int[] reporterIntensities)>
+            {
+                (7, new[]{30,56,49}),
+                (3, new[]{97,45,86}),
+                (6, new[]{44,59,61}),
+                (1, new[]{86,32,35}),
+                (8, new[]{13,31,35}),
+                (6, new[]{18,74,49}),
+                (4, new[]{23,9,87}),
+                (4, new[]{63,63,12}),
+                (9, new[]{96,84,0}),
+                (3, new[]{54,53,54}),
+                (1, new[]{9,11,24}),
+                (5, new[]{77,25,35})
+            };
+            inputList.Add(input2);
+            IsobaricQuantEngine ibq2 = new IsobaricQuantEngine(inputList);
+            var o8 = ibq2.Process(aggregateType: IsobaricQuantEngine.AggregateType.SumTopN);
+        }
+        [Test]
+        public void ProcessPsms()
+        {
+            string psmFilePath = @"E:\Projects\Mann_11cell_lines\A549\A549_1\2025-12-02-13-52-34\Task1-SearchTask\AllPSMs.psmtsv";
+            List<PsmFromTsv> parsedPsms = SpectrumMatchTsvReader.ReadPsmTsv(psmFilePath, out var warnings);
+            var input = new List<(int peptideFullSequenceHash, int[] reporterIntensities)>();
+            int counter = 0;
+            foreach (var psm in parsedPsms)
+            {
+                input.Add((peptideFullSequenceHash: psm.FullSequence.GetHashCode(), reporterIntensities: RandomIntegerArray(6, 50, 100)));
+                counter++;
+                if (counter >= 20000)
+                {
+                    break;
+                }
+            }
+            var inputList = new List<List<(int peptideFullSequenceHash, int[] reporterIntensities)>> { input };
+            IsobaricQuantEngine ibq = new IsobaricQuantEngine(inputList);
+            var o1 = ibq.Process(aggregateType: IsobaricQuantEngine.AggregateType.SumTopN);
+
+            psmFilePath = @"E:\Projects\Mann_11cell_lines\A549\A549_1\2025-12-02-13-54-13\Task1-SearchTask\AllPSMs.psmtsv";
+            parsedPsms = SpectrumMatchTsvReader.ReadPsmTsv(psmFilePath, out warnings);
+            input = new List<(int peptideFullSequenceHash, int[] reporterIntensities)>();
+            counter = 0;
+            foreach (var psm in parsedPsms)
+            {
+                input.Add((peptideFullSequenceHash: psm.FullSequence.GetHashCode(), reporterIntensities: RandomIntegerArray(6, 50, 100)));
+                counter++;
+                if (counter >= 20000)
+                {
+                    break;
+                }
+            }
+            inputList = new List<List<(int peptideFullSequenceHash, int[] reporterIntensities)>> { input };
+            var ibq2 = new IsobaricQuantEngine(inputList);
+            var o2 = ibq.Process(aggregateType: IsobaricQuantEngine.AggregateType.SumTopN);
+            int[] newChannelLabels1 = new int[]
+            {
+                "A549_1".GetHashCode(),
+                "A549_2".GetHashCode(),
+                "A549_3".GetHashCode(),
+                "A549_4".GetHashCode(),
+                "A549_5".GetHashCode(),
+                "A549_6".GetHashCode()
+            };
+            var r1 = ibq.ReplaceChannelIndexBySampleKey(o1, newChannelLabels1);
+            var r2 = ibq2.ReplaceChannelIndexBySampleKey(o2, newChannelLabels1);
+            var g = ibq.GlobalResults(new List<ConcurrentDictionary<int, ConcurrentDictionary<int, int>>> { r1, r2 });
+        }
+        [Test]
+        public void ProcessProteinPsms()
+        {
+            string psmFilePath = @"E:\Projects\Mann_11cell_lines\A549\A549_1\2025-12-02-13-52-34\Task1-SearchTask\AllPSMs.psmtsv";
+            List<PsmFromTsv> parsedPsms = SpectrumMatchTsvReader.ReadPsmTsv(psmFilePath, out var warnings);
+            var input = new List<(int peptideFullSequenceHash, int[] reporterIntensities)>();
+            int counter = 0;
+            foreach (var psm in parsedPsms)
+            {
+                input.Add((peptideFullSequenceHash: psm.ProteinAccession.GetHashCode(), reporterIntensities: RandomIntegerArray(6, 50, 100)));
+                counter++;
+                if (counter >= 20000)
+                {
+                    break;
+                }
+            }
+            var inputList = new List<List<(int peptideFullSequenceHash, int[] reporterIntensities)>> { input };
+            IsobaricQuantEngine ibq = new IsobaricQuantEngine(inputList);
+            var o1 = ibq.Process(aggregateType: IsobaricQuantEngine.AggregateType.SumTopN);
+
+            psmFilePath = @"E:\Projects\Mann_11cell_lines\A549\A549_1\2025-12-02-13-54-13\Task1-SearchTask\AllPSMs.psmtsv";
+            parsedPsms = SpectrumMatchTsvReader.ReadPsmTsv(psmFilePath, out warnings);
+            input = new List<(int peptideFullSequenceHash, int[] reporterIntensities)>();
+            counter = 0;
+            foreach (var psm in parsedPsms)
+            {
+                input.Add((peptideFullSequenceHash: psm.ProteinAccession.GetHashCode(), reporterIntensities: RandomIntegerArray(6, 50, 100)));
+                counter++;
+                if (counter >= 20000)
+                {
+                    break;
+                }
+            }
+            inputList = new List<List<(int peptideFullSequenceHash, int[] reporterIntensities)>> { input };
+            var ibq2 = new IsobaricQuantEngine(inputList);
+            var o2 = ibq.Process(aggregateType: IsobaricQuantEngine.AggregateType.SumTopN);
+            int[] newChannelLabels1 = new int[]
+            {
+                "A549_1".GetHashCode(),
+                "A549_2".GetHashCode(),
+                "A549_3".GetHashCode(),
+                "A549_4".GetHashCode(),
+                "A549_5".GetHashCode(),
+                "A549_6".GetHashCode()
+            };
+            var r1 = ibq.ReplaceChannelIndexBySampleKey(o1, newChannelLabels1);
+            var r2 = ibq2.ReplaceChannelIndexBySampleKey(o2, newChannelLabels1);
+            var g = ibq.GlobalResults(new List<ConcurrentDictionary<int, ConcurrentDictionary<int, int>>> { r1, r2 });
+        }
+        public int[] RandomIntegerArray(int length, int minValue, int maxValue)
+        {
+            Random rand = new Random();
+            int[] array = new int[length];
+            for (int i = 0; i < length; i++)
+            {
+                array[i] = rand.Next(minValue, maxValue);
+            }
+            return array;
+        }
+    }
+}
+

mzLib/Test/Test.csproj

@@ -26,6 +26,7 @@
     <ProjectReference Include="..\BayesianEstimation\BayesianEstimation.csproj" />
     <ProjectReference Include="..\Chemistry\Chemistry.csproj" />
     <ProjectReference Include="..\FlashLFQ\FlashLFQ.csproj" />
+    <ProjectReference Include="..\IsobaricQuant\IsobaricQuant.csproj" />
     <ProjectReference Include="..\MassSpectrometry\MassSpectrometry.csproj" />
     <ProjectReference Include="..\MzIdentML\MzIdentML.csproj" />
     <ProjectReference Include="..\Omics\Omics.csproj" />