not working

mzLib/Omics/Fragmentation/MatchedFragmentIon.cs

@@ -5,15 +5,15 @@ namespace Omics.Fragmentation
 {
     public class MatchedFragmentIon
     {
-        public readonly IProduct NeutralTheoreticalProduct;
+        public readonly Product NeutralTheoreticalProduct;
         public readonly double Mz;
         public readonly double Intensity;
         public readonly int Charge;
 
         /// <summary>
         /// Constructs a new MatchedFragmentIon given information about a theoretical and an experimental fragment mass spectral peak
         /// </summary>
-        public MatchedFragmentIon(ref IProduct neutralTheoreticalProduct, double experMz, double experIntensity, int charge)
+        public MatchedFragmentIon(ref Product neutralTheoreticalProduct, double experMz, double experIntensity, int charge)
         {
             NeutralTheoreticalProduct = neutralTheoreticalProduct;
             Mz = experMz;
@@ -23,7 +23,7 @@ public MatchedFragmentIon(ref IProduct neutralTheoreticalProduct, double experMz
         /// <summary>
         /// Constructs a new MatchedFragmentIon given information about a theoretical and an experimental fragment mass spectral peak
         /// </summary>
-        public MatchedFragmentIon(IProduct neutralTheoreticalProduct, double experMz, double experIntensity, int charge)
+        public MatchedFragmentIon(Product neutralTheoreticalProduct, double experMz, double experIntensity, int charge)
         {
             NeutralTheoreticalProduct = neutralTheoreticalProduct;
             Mz = experMz;

mzLib/Omics/Fragmentation/Product.cs

@@ -0,0 +1,110 @@
+using System;
+using System.Collections.Generic;
+using System.Linq;
+using System.Text;
+using Chemistry;
+
+namespace Omics.Fragmentation
+{
+    public class Product : IHasMass
+    {
+        public double NeutralMass { get; }
+        public ProductType ProductType { get; }
+        public double NeutralLoss { get; }
+        public FragmentationTerminus Terminus { get; }
+        public int FragmentNumber { get; }
+        public int ResiduePosition { get; }
+        public int AminoAcidPosition => ResiduePosition;
+        public ProductType? SecondaryProductType { get; } //used for internal fragment ions
+        public int SecondaryFragmentNumber { get; } //used for internal fragment ions
+        public double MonoisotopicMass => NeutralMass;
+
+        /// <summary>
+        /// A product is the individual neutral fragment from an MS dissociation. A fragmentation product here contains one of the two termini (N- or C-). 
+        /// The ProductType describes where along the backbone the fragmentaiton occurred (e.g. b-, y-, c-, zdot-). The neutral loss mass (if any) that 
+        /// occurred from a mod on the fragment is listed as a mass. Finally the neutral mass of the whole fragment is provided.
+        /// </summary>
+        public Product(ProductType productType, FragmentationTerminus terminus, double neutralMass,
+            int fragmentNumber, int residuePosition, double neutralLoss, ProductType? secondaryProductType = null,
+            int secondaryFragmentNumber = 0)
+        {
+            NeutralMass = neutralMass;
+            ProductType = productType;
+            NeutralLoss = neutralLoss;
+            Terminus = terminus;
+            FragmentNumber = fragmentNumber;
+            ResiduePosition = residuePosition;
+            SecondaryProductType = secondaryProductType;
+            SecondaryFragmentNumber = secondaryFragmentNumber;
+        }
+
+        public string Annotation
+        {
+            get
+            {
+                StringBuilder sb = new StringBuilder();
+
+                if (SecondaryProductType == null)
+                {
+                    sb.Append(ProductType);
+
+                    // for "normal" fragments this is just the fragment number (e.g., the 3 in the b3 ion)
+                    // for diagnostic ions, it's the m/z assuming z=1
+                    // (e.g., a diagnostic ion with neutral mass 100 Da will be reported as the D101 fragment)
+                    sb.Append(FragmentNumber);
+                }
+                else
+                {
+                    //internal fragment ion, annotation used here: 10.1007/s13361-015-1078-1
+                    //example: yIb[18-36]
+                    sb.Append(ProductType + "I" + SecondaryProductType.Value + "[" + FragmentNumber + "-" + SecondaryFragmentNumber + "]");
+                }
+                if (NeutralLoss != 0)
+                {
+                    sb.Append("-");
+                    sb.Append(NeutralLoss.ToString("F2"));
+                }
+
+                return sb.ToString();
+            }
+        }
+
+        /// <summary>
+        /// Summarizes a Product into a string for debug purposes
+        /// </summary>
+        public override string ToString()
+        {
+            if (SecondaryProductType == null)
+            {
+                return ProductType + "" + FragmentNumber + ";" + NeutralMass.ToString("F5") + "-" +
+                       string.Format("{0:0.##}", NeutralLoss);
+            }
+            else
+            {
+                return ProductType + "I" + SecondaryProductType.Value + "[" + FragmentNumber + "-" +
+                       SecondaryFragmentNumber + "]" + ";" + NeutralMass.ToString("F5") + "-" +
+                       string.Format("{0:0.##}", NeutralLoss);
+            }
+        }
+
+        public override bool Equals(object obj)
+        {
+            return obj is Product other && Equals(other);
+        }
+
+        public bool Equals(Product product)
+        {
+            return this.ProductType.Equals(product.ProductType)
+                   && this.NeutralMass.Equals(product.NeutralMass)
+                   && this.FragmentNumber == product.FragmentNumber
+                   && this.NeutralLoss.Equals(product.NeutralLoss)
+                   && this.SecondaryFragmentNumber == product.SecondaryFragmentNumber
+                   && this.SecondaryProductType == product.SecondaryProductType;
+        }
+
+        public override int GetHashCode()
+        {
+            return NeutralMass.GetHashCode();
+        }
+    }
+}

mzLib/Proteomics/Fragmentation/TerminusSpecificProductTypes.cs → mzLib/Omics/Fragmentation/TerminusSpecificProductTypes.cs

@@ -1,9 +1,4 @@
-using System;
-using System.Collections.Generic;
-using System.Text;
-using Omics.Fragmentation;
-
-namespace Proteomics.Fragmentation
+namespace Omics.Fragmentation
 {
     public class TerminusSpecificProductTypes
     {

mzLib/Omics/Omics.csproj

@@ -2,6 +2,7 @@
 
   <PropertyGroup>
     <TargetFramework>net6.0</TargetFramework>
+	<Platforms>x64</Platforms>
     <ImplicitUsings>enable</ImplicitUsings>
     <Nullable>enable</Nullable>
   </PropertyGroup>

mzLib/Omics/SpectrumMatch/LibrarySpectrum.cs

@@ -1,5 +1,6 @@
 using System.Text;
 using Easy.Common.Extensions;
+using MassSpectrometry.MzSpectra;
 using Omics.Fragmentation;
 
 namespace Omics.SpectrumMatch