Isobaric Quant FileInfo and PlexAnnotation to achieve something analogous to SpectraFileInfo

mzLib/MassSpectrometry/IsobaricQuantFileInfo.cs

@@ -0,0 +1,120 @@
+using System;
+using System.Collections.Generic;
+using System.IO;
+
+
+namespace MassSpectrometry
+{
+    /// <summary>
+    /// Describes an isobaric-quantification input file and the plex annotations for that file.
+    /// Immutable for its core identity (path, plex, fraction, technical replicate and annotations).
+    /// </summary>
+    public class IsobaricQuantFileInfo
+    {
+        /// <summary>
+        /// Create a new instance describing a single isobaric quantification file.
+        /// </summary>
+        /// <param name="fullFilePathWithExtension">Absolute or relative path to the spectra/quant file including extension.</param>
+        /// <param name="plex">The plex identifier (e.g., "TMT10", "TMTpro16") for this file. Null will be normalized to empty string.</param>
+        /// <param name="fraction">Fraction index (1-based) for fractionated experiments.</param>
+        /// <param name="technicalReplicate">Technical replicate index (1-based) for repeated injections/runs.</param>
+        /// <param name="annotations">Ordered list of channel annotations for the file's plex (may be empty).</param>
+        public IsobaricQuantFileInfo(string fullFilePathWithExtension, string plex, int fraction, int technicalReplicate, IReadOnlyList<IsobaricQuantPlexAnnotation> annotations)
+        {
+            FullFilePathWithExtension = fullFilePathWithExtension;
+            Plex = plex ?? string.Empty;
+            Fraction = fraction;
+            TechnicalReplicate = technicalReplicate;
+            Annotations = annotations ?? Array.Empty<IsobaricQuantPlexAnnotation>();
+        }
+
+        /// <summary>
+        /// The path to the data file (for example a .raw or .mzML) including the extension.
+        /// Used as the primary identity for equality and hashing.
+        /// </summary>
+        public string FullFilePathWithExtension { get; }
+
+        /// <summary>
+        /// The plex identifier for this file (for example "TMT10" or "TMTpro16").
+        /// Empty string when not provided.
+        /// </summary>
+        public string Plex { get; }
+
+        /// <summary>
+        /// Fraction index for the file. Uses 1-based indexing to match experimental notation.
+        /// </summary>
+        public int Fraction { get; }             // 1-based
+
+        /// <summary>
+        /// Technical replicate index for the file. Uses 1-based indexing.
+        /// </summary>
+        public int TechnicalReplicate { get; }   // 1-based
+
+        /// <summary>
+        /// All channel annotations for this file's plex (one entry per reporter/tag).
+        /// Immutable reference to the provided read-only list (may be empty).
+        /// </summary>
+        public IReadOnlyList<IsobaricQuantPlexAnnotation> Annotations { get; } // All tags for this file's plex
+
+        /// <summary>
+        /// Returns true when the other object represents the same file path.
+        /// Equality is based on <see cref="FullFilePathWithExtension"/>.
+        /// </summary>
+        /// <param name="obj">Other object to compare.</param>
+        /// <returns>True when <paramref name="obj"/> is an <see cref="IsobaricQuantFileInfo"/> with the same file path.</returns>
+        public override bool Equals(object obj)
+        {
+            if (base.Equals(obj))
+            {
+                return ((IsobaricQuantFileInfo)obj).FullFilePathWithExtension.Equals(FullFilePathWithExtension);
+            }
+
+            return false;
+        }
+
+        /// <summary>
+        /// Returns a stable hash code based on <see cref="FullFilePathWithExtension"/>.
+        /// </summary>
+        /// <returns>Hash code.</returns>
+        public override int GetHashCode()
+        {
+            return FullFilePathWithExtension.GetHashCode();
+        }
+
+        /// <summary>
+        /// Returns the file name (without directory) for display and logging.
+        /// </summary>
+        /// <returns>File name portion of <see cref="FullFilePathWithExtension"/>.</returns>
+        public override string ToString()
+        {
+            return Path.GetFileName(FullFilePathWithExtension);
+        }
+    }
+
+    /// <summary>
+    /// Annotation for a single isobaric reporter/tag within a plex.
+    /// Used to map reporter channels to sample/condition/biological replicate metadata.
+    /// </summary>
+    public class IsobaricQuantPlexAnnotation
+    {
+        /// <summary>
+        /// Reporter tag identifier (e.g., "126", "127N", "128C" or the channel label used by the reader).
+        /// </summary>
+        public string Tag { get; set; } = "";
+
+        /// <summary>
+        /// Human-readable sample name associated with this reporter channel.
+        /// </summary>
+        public string SampleName { get; set; } = "";
+
+        /// <summary>
+        /// Experimental condition or group for this reporter channel (e.g., "Control" or "Treatment").
+        /// </summary>
+        public string Condition { get; set; } = "";
+
+        /// <summary>
+        /// Biological replicate index for this channel (1-based). Zero or negative if not set.
+        /// </summary>
+        public int BiologicalReplicate { get; set; }
+    }
+}

mzLib/Test/Omics/IsobaricQuantFileAndSampleTests.cs

@@ -0,0 +1,49 @@
+using MassSpectrometry;
+using NUnit.Framework;
+using Omics;
+using System.Collections.Generic;
+using System.Diagnostics.CodeAnalysis;
+
+namespace Test.Omics
+{
+    [TestFixture]
+    [ExcludeFromCodeCoverage]
+    internal class IsobaricQuantFileAndSampleTests
+    {
+        [Test]
+        public void TestIsobaricQuantFileAndPlexAnnotationCreation()
+        {
+            // Create annotations for the plex
+            var annotations = new List<IsobaricQuantPlexAnnotation>
+            {
+                new IsobaricQuantPlexAnnotation
+                {
+                    Tag = "126",
+                    SampleName = "Sample1",
+                    Condition = "Control",
+                    BiologicalReplicate = 1
+                }
+            };
+
+            // Create an instance of IsobaricQuantFileInfo
+            var fileInfo = new IsobaricQuantFileInfo(
+                fullFilePathWithExtension: "SampleQuantFile.raw",
+                plex: "TMT10",
+                fraction: 1,
+                technicalReplicate: 1,
+                annotations: annotations);
+
+            // Assert that the properties are set correctly
+            Assert.That(fileInfo.FullFilePathWithExtension, Is.EqualTo("SampleQuantFile.raw"));
+            Assert.That(fileInfo.Plex, Is.EqualTo("TMT10"));
+            Assert.That(fileInfo.Fraction, Is.EqualTo(1));
+            Assert.That(fileInfo.TechnicalReplicate, Is.EqualTo(1));
+            Assert.That(fileInfo.Annotations, Is.Not.Null);
+            Assert.That(fileInfo.Annotations.Count, Is.EqualTo(1));
+            Assert.That(fileInfo.Annotations[0].Tag, Is.EqualTo("126"));
+            Assert.That(fileInfo.Annotations[0].SampleName, Is.EqualTo("Sample1"));
+            Assert.That(fileInfo.Annotations[0].Condition, Is.EqualTo("Control"));
+            Assert.That(fileInfo.Annotations[0].BiologicalReplicate, Is.EqualTo(1));
+        }
+    }
+}