Merge branch 'master' into DbWriterFix

mzLib/Omics/IBioPolymerWithSetMods.cs

@@ -44,29 +44,6 @@ 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);
 

mzLib/Proteomics/ProteolyticDigestion/PeptideWithSetModifications.cs

@@ -16,7 +16,7 @@ namespace Proteomics.ProteolyticDigestion
     [Serializable]
     public class PeptideWithSetModifications : ProteolyticPeptide, IBioPolymerWithSetMods, IEquatable<PeptideWithSetModifications>
     {
-        public string FullSequence { get; private set; } //sequence with modifications
+        public string FullSequence { get; init; } //sequence with modifications
         public int NumFixedMods { get; }
         // Parameter to store the full sequence of the corresponding Target or Decoy peptide
         // If the peptide in question is a decoy, this pairs it to the target it was generated from
@@ -884,6 +884,11 @@ public override string ToString()
             return FullSequence + string.Join("\t", AllModsOneIsNterminus.Select(m => m.ToString()));
         }
 
+        #region IEquatable
+
+        /// <summary>
+        /// Peptides are equal if they have the same full sequence, parent, and digestion agent
+        /// </summary>
         public override bool Equals(object obj)
         {
             if (obj is PeptideWithSetModifications peptide)
@@ -893,12 +898,29 @@ public override bool Equals(object obj)
             return false;
         }
 
+        /// <summary>
+        /// Peptides are equal if they have the same full sequence, parent, and digestion agent
+        /// </summary>
+        public bool Equals(IBioPolymerWithSetMods other) => Equals(other as PeptideWithSetModifications);
+
+        /// <summary>
+        /// Peptides are equal if they have the same full sequence, parent, and digestion agent
+        /// </summary>
         public bool Equals(PeptideWithSetModifications other)
         {
-            // interface equals first because it does null and reference checks
-            return (this as IBioPolymerWithSetMods).Equals(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)
+                   // These last two are important for parsimony in MetaMorpheus
                    && OneBasedStartResidue == other!.OneBasedStartResidue
-                   && Equals(Parent, other.Parent);
+                   && Equals(Parent?.Accession, other.Parent?.Accession); 
         }
 
         public override int GetHashCode()
@@ -917,6 +939,8 @@ public override int GetHashCode()
             return hash.ToHashCode();
         }
 
+        #endregion
+
         /// <summary>
         /// This should be run after deserialization of a PeptideWithSetModifications, in order to set its Protein and Modification objects, which were not serialized
         /// </summary>

mzLib/Test/TestPeptideWithSetMods.cs

@@ -71,6 +71,8 @@ public static void TestPeptideOligoEquality()
             Assert.That(!peptide.Equals(oligo));
             Assert.That(!((IBioPolymerWithSetMods)oligo).Equals(peptide));
             Assert.That(!((IBioPolymerWithSetMods)peptide).Equals(oligo));
+            Assert.That(!((object)oligo).Equals(peptide));
+            Assert.That(!((object)peptide).Equals(oligo));
         }
 
         [Test]
@@ -1194,6 +1196,45 @@ public static void TestPeptideWithSetModsNoParentProtein()
             Assert.AreEqual('-', last.NextResidue);
         }
 
+        [Test]
+        public static void TestPeptideWithSetModsEquals()
+        {
+            // Create two proteins
+            Protein protein1 = new Protein("SEQUENCEK", "accession1");
+            Protein protein2 = new Protein("SEQUENCEK", "accession2");
+
+            // Create digestion parameters
+            DigestionParams digestionParams = new DigestionParams(protease: "trypsin", maxMissedCleavages: 0, initiatorMethionineBehavior: InitiatorMethionineBehavior.Retain);
+
+            // Digest the proteins to get peptides
+            PeptideWithSetModifications peptide1 = protein1.Digest(digestionParams, new List<Modification>(), new List<Modification>()).First();
+            PeptideWithSetModifications peptide2 = protein2.Digest(digestionParams, new List<Modification>(), new List<Modification>()).First();
+
+            // Test equality - same peptide
+            Assert.IsTrue(peptide1.Equals(peptide1));
+
+            // different peptide
+            Assert.IsTrue(!peptide1.Equals(peptide2));
+            Assert.IsTrue(!peptide1.Equals((object)peptide2));
+            Assert.IsTrue(!peptide1.Equals((IBioPolymerWithSetMods)peptide2));
+            Assert.AreNotEqual(peptide1.GetHashCode(), peptide2.GetHashCode());
+
+            // Test inequality with different start residue
+            PeptideWithSetModifications peptide3 = new PeptideWithSetModifications(protein1, digestionParams, 2, 9, CleavageSpecificity.Full, "", 0, new Dictionary<int, Modification>(), 0);
+            Assert.IsFalse(peptide1.Equals(peptide3));
+
+            // Test inequality with different parent accession
+            PeptideWithSetModifications peptide4 = new PeptideWithSetModifications(protein2, digestionParams, 1, 9, CleavageSpecificity.Full, "", 0, new Dictionary<int, Modification>(), 0);
+            Assert.IsFalse(peptide1.Equals(peptide4));
+
+            // all fail on null
+            Assert.That(!peptide1.Equals(null));
+            Assert.That(!peptide1.Equals((object)null));
+            Assert.That(!peptide1.Equals((PeptideWithSetModifications)null));
+        }
+
+
+
         [Test]
         public static void TestIBioPolymerWithSetModsModificationFromFullSequence()
         {

mzLib/Test/Transcriptomics/TestOligoWithSetMods.cs

@@ -91,43 +91,55 @@ public static void TestEquality()
                 .Digest(new RnaDigestionParams(), [], [])
                 .ElementAt(1);
 
-            Assert.That(oligoWithSetMods, Is.EqualTo(oligoWithSetMods2));
+            // same oligos
+            Assert.That(oligoWithSetMods.Equals(oligoWithSetMods2));
+            Assert.That(oligoWithSetMods.Equals((object)oligoWithSetMods2));
+            Assert.That(oligoWithSetMods.Equals((OligoWithSetMods)oligoWithSetMods2));
+            Assert.That(oligoWithSetMods.Equals(oligoWithSetMods));
+            Assert.That(oligoWithSetMods.Equals((object)oligoWithSetMods));
+            Assert.That(oligoWithSetMods.Equals((OligoWithSetMods)oligoWithSetMods));
             Assert.That(oligoWithSetMods.GetHashCode(), Is.EqualTo(oligoWithSetMods2.GetHashCode()));
-            Assert.That(oligoWithSetMods.Equals((object)oligoWithSetMods2)); // Test the Equals(Object obj) method
+
+            // all fail on null
             Assert.That(!oligoWithSetMods2.Equals(null));
+            Assert.That(!oligoWithSetMods2.Equals((object)null));
+            Assert.That(!oligoWithSetMods2.Equals((OligoWithSetMods)null));
 
             // Null parent checks
             oligoWithSetMods = new(oligoWithSetMods.FullSequence, modDict.ToDictionary(p => p.Value.First().IdWithMotif, p => p.Value.First()));
             oligoWithSetMods2 = new OligoWithSetMods(oligoWithSetMods.FullSequence, modDict.ToDictionary(p => p.Value.First().IdWithMotif, p => p.Value.First()));
             var oligoWithSetMods3 = new OligoWithSetMods(oligoWithSetMods.FullSequence + "AGAUA", modDict.ToDictionary(p => p.Value.First().IdWithMotif, p => p.Value.First()));
 
-            Assert.That(oligoWithSetMods, Is.EqualTo(oligoWithSetMods2));
-            Assert.That(oligoWithSetMods, Is.EqualTo((object)oligoWithSetMods2));
-            Assert.That(oligoWithSetMods, Is.EqualTo((OligoWithSetMods)oligoWithSetMods2));
-            Assert.That(oligoWithSetMods, Is.Not.EqualTo(oligoWithSetMods3));
-            Assert.That(oligoWithSetMods, Is.Not.EqualTo((object)oligoWithSetMods3));
-            Assert.That(oligoWithSetMods, Is.Not.EqualTo((IBioPolymerWithSetMods)oligoWithSetMods3));
+            // same oligo null parent
+            Assert.That(oligoWithSetMods.Equals(oligoWithSetMods2));
+            Assert.That(oligoWithSetMods.Equals((object)oligoWithSetMods2));
+            Assert.That(oligoWithSetMods.Equals((OligoWithSetMods)oligoWithSetMods2));
+
+            // different oligo null parent
+            Assert.That(!oligoWithSetMods.Equals(oligoWithSetMods3));
+            Assert.That(!oligoWithSetMods.Equals((object)oligoWithSetMods3));
+            Assert.That(!oligoWithSetMods.Equals((IBioPolymerWithSetMods)oligoWithSetMods3));
         }
 
         [Test]
         [TestCase("GUACUG", "GUACUGGUACUG", "RNase A")]
         [TestCase("GUAGGAG", "GUAGCAG", "RNase A")]
-        public static void TestEquality_DifferentParentSameDigestionProduct(string sequence1, string sequence2, string enzyme)
+        public static void TestInequality_DifferentParentSameDigestionProduct(string sequence1, string sequence2, string enzyme)
         {
             var digestionParams = new RnaDigestionParams(rnase: enzyme, minLength: 1, maxMissedCleavages: 0);
 
-            var oligo1 = new RNA(sequence1)
+            var oligo1 = new RNA(sequence1, "", "rna1", "", "")
                 .Digest(digestionParams, [], [])
                 .First();
 
-            var oligo2 = new RNA(sequence2)
+            var oligo2 = new RNA(sequence2, "", "rna3", "", "")
                 .Digest(digestionParams, [], [])
                 .First();
 
-            Assert.That(oligo1, Is.EqualTo(oligo2));
+            Assert.That(oligo1, Is.Not.EqualTo(oligo2));
             Assert.That(oligo1.Equals(oligo1));
-            Assert.That(oligo1, Is.EqualTo((object)oligo2));
-            Assert.That(oligo1.GetHashCode(), Is.EqualTo(oligo2.GetHashCode()));
+            Assert.That(oligo1, Is.Not.EqualTo((object)oligo2));
+            Assert.That(oligo1.GetHashCode(), Is.Not.EqualTo(oligo2.GetHashCode()));
         }
 
         /// <summary>

mzLib/Transcriptomics/Digestion/OligoWithSetMods.cs

@@ -215,6 +215,11 @@ public void Fragment(DissociationType dissociationType, FragmentationTerminus fr
                     products.AddRange(GetNeutralFragments(type, sequence));
         }
 
+        #region IEquatable
+
+        /// <summary>
+        /// Oligos are equal if they have the same full sequence, parent, and digestion agent, and terminal caps
+        /// </summary>
         public override bool Equals(object? obj)
         {
             if (obj is OligoWithSetMods oligo)
@@ -224,9 +229,31 @@ public override bool Equals(object? obj)
             return false;
         }
 
+        /// <summary>
+        /// Oligos are equal if they have the same full sequence, parent, and digestion agent, and terminal caps
+        /// </summary>
+        public bool Equals(IBioPolymerWithSetMods? other) => Equals(other as OligoWithSetMods);
+
+        /// <summary>
+        /// Oligos are equal if they have the same full sequence, parent, and digestion agent, and terminal caps
+        /// </summary>
         public bool Equals(OligoWithSetMods? other)
         {
-            return (this as IBioPolymerWithSetMods).Equals(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)
+                   && _fivePrimeTerminus.Equals(other._fivePrimeTerminus)
+                   && _threePrimeTerminus.Equals(other._threePrimeTerminus)
+                   // These last two are important for parsimony in MetaMorpheus
+                   && OneBasedStartResidue == other!.OneBasedStartResidue
+                   && Equals(Parent?.Accession, other.Parent?.Accession);
         }
 
         public override int GetHashCode()
@@ -242,9 +269,13 @@ public override int GetHashCode()
             {
                 hash.Add(DigestionParams.DigestionAgent);
             }
+            hash.Add(FivePrimeTerminus);
+            hash.Add(ThreePrimeTerminus);
             return hash.ToHashCode();
         }
 
+        #endregion
+
         /// <summary>
         /// Generates theoretical internal fragments for given dissociation type for this peptide. 
         /// The "products" parameter is filled with these fragments.

mzLib/Transcriptomics/RNA.cs

@@ -23,7 +23,7 @@ public RNA(string sequence, IHasChemicalFormula? fivePrimeTerm = null, IHasChemi
         /// </summary>
         /// <param name="sequence"></param>
         /// <param name="name"></param>
-        /// <param name="identifier"></param>
+        /// <param name="accession"></param>
         /// <param name="organism"></param>
         /// <param name="databaseFilePath"></param>
         /// <param name="fivePrimeTerminus"></param>
@@ -33,12 +33,12 @@ public RNA(string sequence, IHasChemicalFormula? fivePrimeTerm = null, IHasChemi
         /// <param name="isDecoy"></param>
         /// <param name="geneNames"></param>
         /// <param name="databaseAdditionalFields"></param>
-        public RNA(string sequence, string name, string identifier, string organism, string databaseFilePath,
+        public RNA(string sequence, string name, string accession, string organism, string databaseFilePath,
             IHasChemicalFormula? fivePrimeTerminus = null, IHasChemicalFormula? threePrimeTerminus = null,
             IDictionary<int, List<Modification>>? oneBasedPossibleModifications = null,
             bool isContaminant = false, bool isDecoy = false, List<Tuple<string, string>> geneNames = null,
             Dictionary<string, string>? databaseAdditionalFields = null)
-            : base(sequence, name, identifier, organism, databaseFilePath, fivePrimeTerminus, threePrimeTerminus,
+            : base(sequence, name, accession, organism, databaseFilePath, fivePrimeTerminus, threePrimeTerminus,
                 oneBasedPossibleModifications, isContaminant, isDecoy, geneNames, databaseAdditionalFields)
         {
 

mzLib/mzLib.sln.DotSettings

@@ -8,6 +8,7 @@
 	<s:Boolean x:Key="/Default/UserDictionary/Words/=Modomics/@EntryIndexedValue">True</s:Boolean>
 	<s:Boolean x:Key="/Default/UserDictionary/Words/=Nucleolytic/@EntryIndexedValue">True</s:Boolean>
 	<s:Boolean x:Key="/Default/UserDictionary/Words/=Oligo/@EntryIndexedValue">True</s:Boolean>
+	<s:Boolean x:Key="/Default/UserDictionary/Words/=Oligos/@EntryIndexedValue">True</s:Boolean>
 	<s:Boolean x:Key="/Default/UserDictionary/Words/=Prsm/@EntryIndexedValue">True</s:Boolean>
 	<s:Boolean x:Key="/Default/UserDictionary/Words/=Regexes/@EntryIndexedValue">True</s:Boolean>
 	<s:Boolean x:Key="/Default/UserDictionary/Words/=Toppic/@EntryIndexedValue">True</s:Boolean>