OSM can read in terminal caps

mzLib/Chemistry/ChemicalFormula.cs

@@ -33,7 +33,7 @@ namespace Chemistry
     /// Formula can change!!! If isotopes or elements are changed.
     /// </summary>
     [Serializable]
-    public sealed class ChemicalFormula : IEquatable<ChemicalFormula>, IHasChemicalFormula
+    public sealed class ChemicalFormula : IEquatable<ChemicalFormula>, IEquatable<IHasChemicalFormula>, IHasChemicalFormula
     {
         // Main data stores, the isotopes and elements
 
@@ -487,6 +487,8 @@ public bool Equals(ChemicalFormula other)
             return true;
         }
 
+        public bool Equals(IHasChemicalFormula other) => Equals(other?.ThisChemicalFormula);
+
         /// <summary>
         /// Produces the Hill Notation of the chemical formula
         /// </summary>

mzLib/Readers/InternalResults/IndividualResultRecords/OsmFromTsv.cs

@@ -1,24 +1,46 @@
-using Omics.SpectrumMatch;
+using Chemistry;
+using Omics.SpectrumMatch;
+using Transcriptomics;
+using Transcriptomics.Digestion;
 
 namespace Readers
 {
     public class OsmFromTsv : SpectrumMatchFromTsv
     {
+        public IHasChemicalFormula FivePrimeTerminus { get; set; }
+        public IHasChemicalFormula ThreePrimeTerminus { get; set; }
+
         public OsmFromTsv(string line, char[] split, Dictionary<string, int> parsedHeader)
             : base(line, split, parsedHeader)
         {
-            // TODO: Parse Oligo specific columns
+            var spl = line.Split(split).Select(p => p.Trim('\"')).ToArray();
+
+            if (parsedHeader[SpectrumMatchFromTsvHeader.FivePrimeTerminus] >= 0)
+                FivePrimeTerminus = ChemicalFormula.ParseFormula(spl[parsedHeader[SpectrumMatchFromTsvHeader.FivePrimeTerminus]]);
+            else if (PreviousResidue == "-")
+                FivePrimeTerminus = NucleicAcid.DefaultFivePrimeTerminus;
+            else
+                FivePrimeTerminus = Rnase.DefaultFivePrimeTerminus;
+
+            if (parsedHeader[SpectrumMatchFromTsvHeader.ThreePrimeTerminus] >= 0)
+                ThreePrimeTerminus = ChemicalFormula.ParseFormula(spl[parsedHeader[SpectrumMatchFromTsvHeader.ThreePrimeTerminus]]);
+            else if (NextResidue == "-")
+                ThreePrimeTerminus = NucleicAcid.DefaultThreePrimeTerminus;
+            else
+                ThreePrimeTerminus = Rnase.DefaultThreePrimeTerminus;
         }
 
         /// <summary>
-        /// Constructor used to disambiguate PsmFromTsv to a single psm object
+        /// Constructor used to disambiguate PsmFromTsv to a single osm object
         /// </summary>
-        /// <param name="psm">psm to disambiguate</param>
-        /// <param name="fullSequence">sequence of ambiguous psm to use</param>
-        public OsmFromTsv(OsmFromTsv psm, string fullSequence, int index = 0, string baseSequence = "")
-            : base(psm, fullSequence, index, baseSequence)
+        /// <param name="osm">osm to disambiguate</param>
+        /// <param name="fullSequence">sequence of ambiguous osm to use</param>
+        public OsmFromTsv(OsmFromTsv osm, string fullSequence, int index = 0, string baseSequence = "",
+            IHasChemicalFormula? fivePrimeTerm = null, IHasChemicalFormula? threePrimeTerm = null)
+            : base(osm, fullSequence, index, baseSequence)
         {
-            // TODO: Parse Oligo specific columns
+            FivePrimeTerminus = fivePrimeTerm ?? osm.FivePrimeTerminus;
+            ThreePrimeTerminus = threePrimeTerm ?? osm.ThreePrimeTerminus;
         }
     }
 }

mzLib/Readers/InternalResults/IndividualResultRecords/SpectrumMatchFromTsvHeader.cs

@@ -116,5 +116,9 @@ public class SpectrumMatchFromTsvHeader
         public const string AllPotentialGlycanLocalization = "All Potential Glycan Localizations";
         public const string AllSiteSpecificLocalizationProbability = "All SiteSpecific Localization Probability";
         public const string LocalizationScore = "Localization Score";
+
+        // Oligo
+        public const string FivePrimeTerminus = "5'-Terminus";
+        public const string ThreePrimeTerminus = "3'-Terminus";
     }
 }

mzLib/Readers/InternalResults/ResultFiles/SpectrumMatchTsvReader.cs

@@ -215,7 +215,7 @@ public static Dictionary<string, int> ParseHeader(string header)
             parsedHeader.Add(SpectrumMatchFromTsvHeader.ParentIonsLabel, Array.IndexOf(spl, SpectrumMatchFromTsvHeader.ParentIonsLabel));
             parsedHeader.Add(SpectrumMatchFromTsvHeader.Ms2ScanRetentionTime, Array.IndexOf(spl, SpectrumMatchFromTsvHeader.Ms2ScanRetentionTime));
 
-
+            // Glyco
             parsedHeader.Add(SpectrumMatchFromTsvHeader.GlycanMass, Array.IndexOf(spl, SpectrumMatchFromTsvHeader.GlycanMass));
             parsedHeader.Add(SpectrumMatchFromTsvHeader.GlycanStructure, Array.IndexOf(spl, SpectrumMatchFromTsvHeader.GlycanStructure));
             parsedHeader.Add(SpectrumMatchFromTsvHeader.GlycanComposition, Array.IndexOf(spl, SpectrumMatchFromTsvHeader.GlycanComposition));
@@ -247,6 +247,11 @@ public static Dictionary<string, int> ParseHeader(string header)
             {
                 parsedHeader[SpectrumMatchFromTsvHeader.AllSiteSpecificLocalizationProbability] = Array.IndexOf(spl, "AllSiteSpecificLocalizationProbability");
             }
+
+            // Oligo
+            parsedHeader.Add(SpectrumMatchFromTsvHeader.FivePrimeTerminus, Array.IndexOf(spl, SpectrumMatchFromTsvHeader.FivePrimeTerminus));
+            parsedHeader.Add(SpectrumMatchFromTsvHeader.ThreePrimeTerminus, Array.IndexOf(spl, SpectrumMatchFromTsvHeader.ThreePrimeTerminus));
+
             return parsedHeader;
         }
 

mzLib/Test/TestChemicalFormula.cs

@@ -374,12 +374,42 @@ public static void FormulaValueEquality()
         }
 
         [Test]
-        public static void FormulaEquality()
+        public static void FormulaEquality_AreEqual_SameReference()
         {
             ChemicalFormula formulaA = ChemicalFormula.ParseFormula("C2H3NO");
             Assert.AreEqual(formulaA, formulaA);
         }
 
+        [Test]
+        public static void FormulaEquality_AreEqual_DifferentReference()
+        {
+            ChemicalFormula formulaA = ChemicalFormula.ParseFormula("C2H3NO");
+            ChemicalFormula formulaB = ChemicalFormula.ParseFormula("C2H3NO");
+            Assert.AreEqual(formulaA, formulaB);
+        }
+
+        [Test]
+        public static void FormulaEquality_Rearranged()
+        {
+            ChemicalFormula formulaA = ChemicalFormula.ParseFormula("C2H3NO");
+            ChemicalFormula formulaB = ChemicalFormula.ParseFormula("H3NOC2");
+            Assert.AreEqual(formulaA, formulaB);
+        }
+
+        [Test]
+        public static void FormulaEquality_null()
+        {
+            ChemicalFormula formulaA = ChemicalFormula.ParseFormula("C2H3NO");
+            Assert.AreNotEqual(formulaA, null);
+        }
+
+        [Test]
+        public static void FormulaEquality_OtherType()
+        {
+            ChemicalFormula formulaA = ChemicalFormula.ParseFormula("C2H3NO");
+            Assert.AreNotEqual(formulaA, "C2H3NO");
+        }
+
         [Test]
         public static void FormulaAlmostEquality()
         {
@@ -388,6 +418,30 @@ public static void FormulaAlmostEquality()
             Assert.AreNotEqual(formulaA, formulaB);
         }
 
+        [Test]
+        public static void FormulaEquality_AreEqual_DifferentReference_Interface()
+        {
+            ChemicalFormula formulaA = ChemicalFormula.ParseFormula("C2H3NO");
+            IHasChemicalFormula formulaB = ChemicalFormula.ParseFormula("C2H3NO");
+            Assert.IsTrue(formulaA.Equals(formulaB));
+        }
+
+        [Test]
+        public static void FormulaEquality_Rearranged_Interface()
+        {
+            ChemicalFormula formulaA = ChemicalFormula.ParseFormula("C2H3NO");
+            IHasChemicalFormula formulaB = ChemicalFormula.ParseFormula("H3NOC2");
+            Assert.IsTrue(formulaA.Equals(formulaB));
+        }
+
+        [Test]
+        public static void FormulaAlmostEquality_Interface()
+        {
+            ChemicalFormula formulaA = ChemicalFormula.ParseFormula("C2H3NO");
+            IHasChemicalFormula formulaB = ChemicalFormula.ParseFormula("C{12}2H3NO");
+            Assert.IsFalse(formulaA.Equals(formulaB));
+        }
+
         [Test]
         public static void HashCodeEquality()
         {