good midpont

mzLib/Omics/Fragmentation/IProduct.cs

@@ -3,20 +3,51 @@
 using System.Linq;
 using System.Text;
 using System.Threading.Tasks;
+using Chemistry;
 
 namespace Omics.Fragmentation
 {
-    public interface IProduct
+    public interface IProduct : IHasMass, IEquatable<IProduct>
     {
         double NeutralMass { get; }
         ProductType ProductType { get; }
         double NeutralLoss { get; }
         FragmentationTerminus Terminus { get; }
         int FragmentNumber { get; }
-        int Position { get; }
+        int ResiduePosition { get; }
         ProductType? SecondaryProductType { get; } //used for internal fragments
         int SecondaryFragmentNumber { get; } //used for internal fragment ions
-        string Annotation { get; }
+        string Annotation => GetAnnotation();
+        string GetAnnotation()
+        {
+                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();
+
+        }
+
+        string ToString();
+        int GetHashCode();
     }
 }

mzLib/Omics/ISpectrumMatch.cs

@@ -4,6 +4,7 @@
 using System.Text;
 using System.Text.RegularExpressions;
 using System.Threading.Tasks;
+using Omics.Fragmentation;
 
 namespace Omics
 {

mzLib/Proteomics/Fragmentation/DissociationTypeCollection.cs

@@ -3,6 +3,7 @@
 using MassSpectrometry;
 using System.Collections.Generic;
 using System.Linq;
+using Omics.Fragmentation;
 
 namespace Proteomics.Fragmentation
 {

mzLib/Proteomics/Fragmentation/Product.cs

@@ -1,67 +1,41 @@
 using System;
 using System.Text;
+using Omics.Fragmentation;
 
 namespace Proteomics.Fragmentation
 {
-    public struct Product
+    public class Product : IProduct
     {
-        public readonly double NeutralMass;
-        public readonly ProductType ProductType;
-        public readonly double NeutralLoss;
-        public readonly FragmentationTerminus Terminus;
-        public readonly int FragmentNumber;
-        public readonly int AminoAcidPosition;
-        public readonly ProductType? SecondaryProductType; //used for internal fragment ions
-        public readonly int SecondaryFragmentNumber; //used for internal fragment ions
+        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,
+    /// <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 aminoAcidPosition, double neutralLoss, ProductType? secondaryProductType = null, int secondaryFragmentNumber = 0)
         {
             NeutralMass = neutralMass;
             ProductType = productType;
             NeutralLoss = neutralLoss;
             Terminus = terminus;
             FragmentNumber = fragmentNumber;
-            AminoAcidPosition = aminoAcidPosition;
+            ResiduePosition = aminoAcidPosition;
             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();
-            }
-        }
+        public string Annotation => (this as IProduct).GetAnnotation();
+
 
         /// <summary>
         /// Summarizes a Product into a string for debug purposes
@@ -80,14 +54,17 @@ public override string ToString()
 
         public override bool Equals(object obj)
         {
-            Product other = (Product)obj;
+            return obj is Product other && Equals(other);
+        }
 
-            return this.ProductType == other.ProductType
-                && this.NeutralMass == other.NeutralMass
-                && this.FragmentNumber == other.FragmentNumber
-                && this.NeutralLoss == other.NeutralLoss
-                && this.SecondaryFragmentNumber == other.SecondaryFragmentNumber
-                && this.SecondaryProductType == other.SecondaryProductType;
+        public bool Equals(IProduct 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()

mzLib/Proteomics/Fragmentation/TerminusSpecificProductTypes.cs

@@ -1,6 +1,7 @@
 using System;
 using System.Collections.Generic;
 using System.Text;
+using Omics.Fragmentation;
 
 namespace Proteomics.Fragmentation
 {

mzLib/Proteomics/PSM/LibrarySpectrum.cs

@@ -1,6 +1,6 @@
 using Easy.Common.Extensions;
 using MassSpectrometry.MzSpectra;
-using Proteomics.Fragmentation;
+using Omics.Fragmentation;
 using System;
 using System.Collections.Generic;
 using System.Linq;

mzLib/Proteomics/PSM/PsmFromTsv.cs

@@ -9,6 +9,7 @@
 using System.Text;
 using System.Text.RegularExpressions;
 using System.Threading.Tasks;
+using Omics.Fragmentation;
 
 namespace Proteomics.PSM
 {

mzLib/Proteomics/Protein/Protein.cs

@@ -4,6 +4,7 @@
 using System.Collections.Generic;
 using System.Linq;
 using System.Text.RegularExpressions;
+using Omics.Fragmentation;
 
 namespace Proteomics
 {

mzLib/Proteomics/ProteolyticDigestion/DigestionParams.cs

@@ -1,5 +1,6 @@
 using Proteomics.Fragmentation;
 using System;
+using Omics.Fragmentation;
 
 namespace Proteomics.ProteolyticDigestion
 {

mzLib/Proteomics/ProteolyticDigestion/PeptideWithSetModifications.cs

@@ -6,8 +6,9 @@
 using System.Collections.Generic;
 using System.Linq;
 using System.Text;
+ using Omics.Fragmentation;
 
-namespace Proteomics.ProteolyticDigestion
+ namespace Proteomics.ProteolyticDigestion
 {
     [Serializable]
     public class PeptideWithSetModifications : ProteolyticPeptide

mzLib/Proteomics/ProteolyticDigestion/ProductTypeMethods.cs

@@ -1,6 +1,6 @@
-using Proteomics.Fragmentation;
-using System;
+using System;
 using System.Collections.Generic;
+using Omics.Fragmentation;
 
 namespace Proteomics.ProteolyticDigestion
 {