IEquality Hotfix (#817)

* fixed bugs

* More Equality Tests

* One More Time

* Digestion Agent Equality and additional comments

* updated protease and expanded test coverage

---------

Co-authored-by: Nic Bollis <nbollis@wisc.edu>

mzLib/Omics/Digestion/DigestionAgent.cs

@@ -1,9 +1,4 @@
 using Omics.Modifications;
-using System;
-using System.Collections.Generic;
-using System.Linq;
-using System.Text;
-using System.Threading.Tasks;
 
 namespace Omics.Digestion
 {
@@ -17,7 +12,7 @@ protected DigestionAgent(string name, CleavageSpecificity cleavageSpecificity, L
             CleavageMod = cleavageMod;
         }
 
-        public string Name { get; init; }
+        public readonly string Name;
         public CleavageSpecificity CleavageSpecificity { get; init; }
         public List<DigestionMotif> DigestionMotifs { get; init; }
         public Modification CleavageMod { get; set; }
@@ -27,6 +22,16 @@ public override string ToString()
             return Name;
         }
 
+        public override bool Equals(object? obj)
+        {
+            return obj is DigestionAgent agent && agent.Name == Name;
+        }
+
+        public override int GetHashCode()
+        {
+            return Name.GetHashCode();
+        }
+
         /// <summary>
         /// Is length of given peptide okay, given minimum and maximum?
         /// </summary>

mzLib/Omics/IBioPolymer.cs

@@ -29,5 +29,14 @@ public interface IBioPolymer : IEquatable<IBioPolymer>
 
         IEnumerable<IBioPolymerWithSetMods> Digest(IDigestionParams digestionParams, List<Modification> allKnownFixedModifications,
             List<Modification> variableModifications, List<SilacLabel> silacLabels = null, (SilacLabel startLabel, SilacLabel endLabel)? turnoverLabels = null, bool topDownTruncationSearch = false);
+
+        bool IEquatable<IBioPolymer>.Equals(IBioPolymer? other)
+        {
+            if (other is null) return false;
+            if (ReferenceEquals(this, other)) return true;
+            if (other.GetType() != GetType()) return false;
+            return Accession == other.Accession
+                && BaseSequence == other.BaseSequence;
+        }
     }
 }

mzLib/Omics/IBioPolymerWithSetMods.cs

@@ -44,6 +44,29 @@ public interface IBioPolymerWithSetMods : IHasChemicalFormula, IEquatable<IBioPo
         char this[int zeroBasedIndex] => BaseSequence[zeroBasedIndex];
         IBioPolymer Parent { get; }
 
+        /// <summary>
+        /// Default Equals Method for IBioPolymerWithSetMods
+        /// </summary>
+        /// <param name="other"></param>
+        /// <returns></returns>
+        /// <remarks>
+        /// Different parent but same sequence and digestion condition => are equal
+        /// Different Digestion agent but same sequence => are not equal (this is for multi-protease analysis in MetaMorpheus)
+        /// </remarks>
+        bool IEquatable<IBioPolymerWithSetMods>.Equals(IBioPolymerWithSetMods? other)
+        {
+            if (other is null) return false;
+            if (ReferenceEquals(this, other)) return true;
+            if (other.GetType() != GetType()) return false;
+
+            // for those constructed from sequence and mods only
+            if (Parent is null && other.Parent is null)
+                return FullSequence.Equals(other.FullSequence);
+
+            return FullSequence == other.FullSequence
+                && Equals(DigestionParams?.DigestionAgent, other.DigestionParams?.DigestionAgent);
+        }
+
         public void Fragment(DissociationType dissociationType, FragmentationTerminus fragmentationTerminus,
             List<Product> products);
 
@@ -163,10 +186,5 @@ public static Dictionary<int, Modification> GetModificationDictionaryFromFullSeq
         /// <returns></returns>
         public static List<Modification> GetModificationsFromFullSequence(string fullSequence,
             Dictionary<string, Modification> allModsKnown) => [.. GetModificationDictionaryFromFullSequence(fullSequence, allModsKnown).Values];
-
-        public bool Equals(IBioPolymerWithSetMods other);
-
-        public int GetHashCode();
-
     }
 }

mzLib/Proteomics/Protein/Protein.cs

@@ -12,7 +12,7 @@
 
 namespace Proteomics
 {
-    public class Protein : IBioPolymer
+    public class Protein : IBioPolymer, IEquatable<Protein>
     {
         private List<ProteolysisProduct> _proteolysisProducts;
 
@@ -969,16 +969,18 @@ public int CompareTo(Protein other)
         //not sure if we require any additional fields for equality
         public override bool Equals(object obj)
         {
-            Protein otherProtein = (Protein)obj;
-            return otherProtein != null && otherProtein.Accession.Equals(Accession) && otherProtein.BaseSequence.Equals(BaseSequence);
+            if (obj is Protein bioPol)
+            {
+                return Equals(bioPol);
+            }
+            return false;
         }
 
-        public bool Equals(IBioPolymer other)
+        public bool Equals(Protein other)
         {
-            Protein otherProtein = (Protein)other;
-            return otherProtein != null && otherProtein.Accession.Equals(Accession) && otherProtein.BaseSequence.Equals(BaseSequence);
+            return (this as IBioPolymer).Equals(other);   
         }
-
+        
         /// <summary>
         /// The protein object uses the default hash code method for speed,
         /// but note that two protein objects with the same information will give two different hash codes.

mzLib/Proteomics/ProteolyticDigestion/PeptideWithSetModifications.cs

@@ -14,7 +14,7 @@
 namespace Proteomics.ProteolyticDigestion
 {
     [Serializable]
-    public class PeptideWithSetModifications : ProteolyticPeptide, IBioPolymerWithSetMods
+    public class PeptideWithSetModifications : ProteolyticPeptide, IBioPolymerWithSetMods, IEquatable<PeptideWithSetModifications>
     {
         public string FullSequence { get; private set; } //sequence with modifications
         public int NumFixedMods { get; }
@@ -886,30 +886,29 @@ public override string ToString()
 
         public override bool Equals(object obj)
         {
-            var q = obj as PeptideWithSetModifications;
-            if (q == null) return false;
-            return Equals(q);
+            if (obj is PeptideWithSetModifications peptide)
+            {
+                return Equals(peptide);
+            }
+            return false;
         }
 
-        public bool Equals(IBioPolymerWithSetMods other)
+        public bool Equals(PeptideWithSetModifications other)
         {
-            return FullSequence == other.FullSequence
-                && OneBasedStartResidue == other.OneBasedStartResidue
-                && ((Parent != null && Parent.Equals(other.Parent)) || (Parent == null & other.Parent == null))
-                && ((DigestionParams?.DigestionAgent != null && DigestionParams.DigestionAgent.Equals(other.DigestionParams?.DigestionAgent))
-                    || (DigestionParams?.DigestionAgent == null & other.DigestionParams?.DigestionAgent == null)); 
+            // interface equals first because it does null and reference checks
+            return (this as IBioPolymerWithSetMods).Equals(other)
+                   && OneBasedStartResidue == other!.OneBasedStartResidue
+                   && Equals(Parent, other.Parent);
         }
 
         public override int GetHashCode()
         {
             var hash = new HashCode();
             hash.Add(FullSequence);
             hash.Add(OneBasedStartResidue);
-            if (Parent != null)
+            if (Parent?.Accession != null)
             {
-                hash.Add(Parent);
-                if (Parent.Accession != null)
-                    hash.Add(Parent.Accession);
+                hash.Add(Parent.Accession);
             }
             if (DigestionParams?.DigestionAgent != null)
             {

mzLib/Proteomics/ProteolyticDigestion/Protease.cs

@@ -24,17 +24,6 @@ public override string ToString()
             return Name;
         }
 
-        public override bool Equals(object obj)
-        {
-            return obj is Protease a
-                && (a.Name == null && Name == null || a.Name.Equals(Name));
-        }
-
-        public override int GetHashCode()
-        {
-            return (Name ?? "").GetHashCode();
-        }
-
         /// <summary>
         /// This method is used to determine cleavage specificity if the cleavage specificity is unknown
         /// This occurs in the speedy nonspecific/semispecific searches when digesting post-search

mzLib/Test/DigestionAgentTests.cs

@@ -0,0 +1,13 @@
+using Omics.Digestion;
+using Omics.Modifications;
+using System.Collections.Generic;
+using NUnit.Framework;
+
+namespace Test
+{
+    public class DigestionAgentTests
+    {
+
+
+    }
+}

mzLib/Test/TestDigestionMotif.cs

@@ -595,5 +595,49 @@ public void TestDigestionParamsMaskedProperties()
             digestionParams.MaxModsForPeptide = 3;
             Assert.That(digestionParams.MaxMods, Is.EqualTo(digestionParams.MaxModsForPeptide));
         }
+
+        private class TestDigestionAgent : DigestionAgent
+        {
+            public TestDigestionAgent(string name, CleavageSpecificity cleavageSpecificity, List<DigestionMotif> motifList, Modification cleavageMod)
+                : base(name, cleavageSpecificity, motifList, cleavageMod)
+            {
+            }
+        }
+
+        [Test]
+        public void Equals_SameName_ReturnsTrue()
+        {
+            var agent1 = ProteaseDictionary.Dictionary["trypsin"];
+            var agent2 = ProteaseDictionary.Dictionary["trypsin"];
+
+            Assert.That(agent1.Equals(agent2), Is.True);
+        }
+
+        [Test]
+        public void Equals_DifferentName_ReturnsFalse()
+        {
+            var agent1 = ProteaseDictionary.Dictionary["trypsin"];
+            var agent2 = ProteaseDictionary.Dictionary["Arg-C"];
+
+            Assert.That(agent1.Equals(agent2), Is.False);
+        }
+
+        [Test]
+        public void GetHashCode_SameName_ReturnsSameHashCode()
+        {
+            var agent1 = ProteaseDictionary.Dictionary["trypsin"];
+            var agent2 = ProteaseDictionary.Dictionary["trypsin"];
+
+            Assert.That(agent1.GetHashCode(), Is.EqualTo(agent2.GetHashCode()));
+        }
+
+        [Test]
+        public void GetHashCode_DifferentName_ReturnsDifferentHashCode()
+        {
+            var agent1 = ProteaseDictionary.Dictionary["trypsin"];
+            var agent2 = ProteaseDictionary.Dictionary["Arg-C"];
+
+            Assert.That(agent1.GetHashCode(), Is.Not.EqualTo(agent2.GetHashCode()));
+        }
     }
 }

mzLib/Test/TestPeptideWithSetMods.cs

@@ -13,6 +13,7 @@
 using Omics.Digestion;
 using Omics.Fragmentation;
 using Omics.Modifications;
+using Transcriptomics.Digestion;
 using UsefulProteomicsDatabases;
 using Stopwatch = System.Diagnostics.Stopwatch;
 
@@ -60,6 +61,18 @@ public static void TestDifferentProteaseEquals()
             Assert.That(!pep1.GetHashCode().Equals(pep2.GetHashCode()));
         }
 
+        [Test]
+        public static void TestPeptideOligoEquality()
+        {
+            var oligo = new OligoWithSetMods("GUACUG", []);
+            var peptide = new PeptideWithSetModifications("PEPTIDE", []);
+
+            Assert.That(!oligo.Equals(peptide));
+            Assert.That(!peptide.Equals(oligo));
+            Assert.That(!((IBioPolymerWithSetMods)oligo).Equals(peptide));
+            Assert.That(!((IBioPolymerWithSetMods)peptide).Equals(oligo));
+        }
+
         [Test]
         public static void TestSemiFewCleavages()
         {

mzLib/Test/TestProteinProperties.cs

@@ -5,8 +5,10 @@
 using System.Collections.Generic;
 using System.IO;
 using System.Linq;
+using Omics;
 using Omics.Modifications;
 using Stopwatch = System.Diagnostics.Stopwatch;
+using Transcriptomics;
 
 namespace Test
 {
@@ -261,5 +263,43 @@ public static void TestProteoformClassification()//string inputPath)
             ///Test case 3 is 2B (not level 3) because you've localized the mod, you just aren't sure what mod it is.
             ///In test case 1, you know what the mods are, but you're not sure where they belong.
         }
+
+        [Test]
+        public void TestProteinEquals()
+        {
+            string sequence = "MKWVTFISLLFLFSSAYSRGVFRRDTHKSEIAHRFKDLGEEHFKGLVLIAFSQYLQQCPFDEHVKLVNEVTEFAKTCVADESAENCDKSLHTLFGDELCKVASLRETYGDMADCCEKQEPERNECFLSHKDDSPDLPKLKPDPNTLCDEFKADEKKFWGKYLYEIARRHPYFYAPELLFFAKRYKAAFTECCQAADKAACLLPKLDELRDEGKASSAKQR";
+            string accession = "P02768";
+            Protein protein1 = new Protein(sequence, accession);
+            Protein protein2 = new Protein(sequence, accession);
+
+            NUnit.Framework.Assert.That(protein1.Equals(protein2), Is.True);
+            NUnit.Framework.Assert.That(protein1.Equals((object)protein2), Is.True);
+            NUnit.Framework.Assert.That(protein1.Equals(null), Is.False);
+        }
+
+        [Test]
+        public void TestProteinGetHashCode()
+        {
+            string sequence = "MKWVTFISLLFLFSSAYSRGVFRRDTHKSEIAHRFKDLGEEHFKGLVLIAFSQYLQQCPFDEHVKLVNEVTEFAKTCVADESAENCDKSLHTLFGDELCKVASLRETYGDMADCCEKQEPERNECFLSHKDDSPDLPKLKPDPNTLCDEFKADEKKFWGKYLYEIARRHPYFYAPELLFFAKRYKAAFTECCQAADKAACLLPKLDELRDEGKASSAKQR";
+            string accession = "P02768";
+            Protein protein = new Protein(sequence, accession);
+
+            NUnit.Framework.Assert.That(protein.GetHashCode(), Is.EqualTo(sequence.GetHashCode()));
+        }
+
+        [Test]
+        public void TestProteinRnaEquality()
+        {
+            string sequence = "MKWVTFISLLFLFSSAYSRGVFRRDTHKSEIAHRFKDLGEEHFKGLVLIAFSQYLQQCPFDEHVKLVNEVTEFAKTCVADESAENCDKSLHTLFGDELCKVASLRETYGDMADCCEKQEPERNECFLSHKDDSPDLPKLKPDPNTLCDEFKADEKKFWGKYLYEIARRHPYFYAPELLFFAKRYKAAFTECCQAADKAACLLPKLDELRDEGKASSAKQR";
+            string accession = "P02768";
+            Protein protein1 = new Protein(sequence, accession);
+            RNA rna = new RNA("GUACUG");
+
+
+            Assert.That(!rna.Equals(protein1));
+            Assert.That(!protein1.Equals(rna));
+            Assert.That(!((IBioPolymer)rna).Equals(protein1));
+            Assert.That(!((IBioPolymer)protein1).Equals(rna));
+        }
     }
 }