Merge branch 'master' into eliminateExtraTabFromChromatographicPeak

mzLib/MassSpectrometry/MsDataScan.cs

@@ -20,6 +20,7 @@
 using System;
 using System.Collections;
 using System.Collections.Generic;
+using System.ComponentModel;
 using System.Linq;
 
 namespace MassSpectrometry
@@ -28,7 +29,7 @@ public class MsDataScan
     {
         public MsDataScan(MzSpectrum massSpectrum, int oneBasedScanNumber, int msnOrder, bool isCentroid, Polarity polarity, double retentionTime, MzRange scanWindowRange, string scanFilter, MZAnalyzerType mzAnalyzer,
             double totalIonCurrent, double? injectionTime, double[,] noiseData, string nativeId, double? selectedIonMz = null, int? selectedIonChargeStateGuess = null, double? selectedIonIntensity = null, double? isolationMZ = null,
-            double? isolationWidth = null, DissociationType? dissociationType = null, int? oneBasedPrecursorScanNumber = null, double? selectedIonMonoisotopicGuessMz = null, string hcdEnergy = null)
+            double? isolationWidth = null, DissociationType? dissociationType = null, int? oneBasedPrecursorScanNumber = null, double? selectedIonMonoisotopicGuessMz = null, string hcdEnergy = null, string scanDescription = null)
         {
             OneBasedScanNumber = oneBasedScanNumber;
             MsnOrder = msnOrder;
@@ -52,6 +53,7 @@ public MsDataScan(MzSpectrum massSpectrum, int oneBasedScanNumber, int msnOrder,
             SelectedIonChargeStateGuess = selectedIonChargeStateGuess;
             SelectedIonMonoisotopicGuessMz = selectedIonMonoisotopicGuessMz;
             HcdEnergy = hcdEnergy;
+            ScanDescription = scanDescription;
         }
 
         /// <summary>
@@ -84,6 +86,7 @@ public MsDataScan(MzSpectrum massSpectrum, int oneBasedScanNumber, int msnOrder,
         public double? SelectedIonMonoisotopicGuessIntensity { get; private set; } // May be refined
         public double? SelectedIonMonoisotopicGuessMz { get; private set; } // May be refined
         public string HcdEnergy { get; private set; }
+        public string ScanDescription { get; private set; }
 
         private MzRange isolationRange;
 

mzLib/Omics/Fragmentation/FragmentationTerminus.cs

@@ -0,0 +1,17 @@
+using System;
+using System.Collections.Generic;
+using System.Linq;
+using System.Text;
+using System.Threading.Tasks;
+
+namespace Omics.Fragmentation
+{
+    public enum FragmentationTerminus
+        {
+            Both, //N- and C-terminus
+            N, //N-terminus only
+            C, //C-terminus only
+            None //used for internal fragments, could be used for top down intact mass?
+        }
+
+}

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

@@ -1,7 +1,7 @@
 using Chemistry;
 using System.Text;
 
-namespace Proteomics.Fragmentation
+namespace Omics.Fragmentation
 {
     public class MatchedFragmentIon
     {
@@ -13,14 +13,13 @@ public class MatchedFragmentIon
         /// <summary>
         /// Constructs a new MatchedFragmentIon given information about a theoretical and an experimental fragment mass spectral peak
         /// </summary>
-        public MatchedFragmentIon(ref Product neutralTheoreticalProduct, double experMz, double experIntensity, int charge)
+        public MatchedFragmentIon(Product neutralTheoreticalProduct, double experMz, double experIntensity, int charge)
         {
             NeutralTheoreticalProduct = neutralTheoreticalProduct;
             Mz = experMz;
             Intensity = experIntensity;
             Charge = charge;
         }
-
         public double MassErrorDa
         {
             get

mzLib/Proteomics/Fragmentation/DissociationTypeCollection.cs → mzLib/Omics/Fragmentation/Peptide/DissociationTypeCollection.cs

@@ -1,10 +1,8 @@
 using Chemistry;
-using Easy.Common.Extensions;
 using MassSpectrometry;
-using System.Collections.Generic;
-using System.Linq;
+using Omics.Fragmentation;
 
-namespace Proteomics.Fragmentation
+namespace Omics.Fragmentation.Peptide
 {
     public class DissociationTypeCollection
     {
@@ -31,7 +29,7 @@ public static List<ProductType> GetTerminusSpecificProductTypesFromDissociation(
                 lock (TerminusSpecificProductTypesFromDissociation)
                 {
                     var productCollection = TerminusSpecificProductTypes.ProductIonTypesFromSpecifiedTerminus[fragmentationTerminus]
-                        .Intersect(DissociationTypeCollection.ProductsFromDissociationType[dissociationType]);
+                        .Intersect(ProductsFromDissociationType[dissociationType]);
 
                     if (!TerminusSpecificProductTypesFromDissociation.TryGetValue((dissociationType, fragmentationTerminus), out productTypes))
                     {

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

@@ -1,8 +1,4 @@
-using System;
-using System.Collections.Generic;
-using System.Text;
-
-namespace Proteomics.Fragmentation
+namespace Omics.Fragmentation.Peptide
 {
     public class TerminusSpecificProductTypes
     {

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

@@ -1,33 +1,36 @@
-using System;
-using System.Text;
+using System.Text;
+using Chemistry;
 
-namespace Proteomics.Fragmentation
+namespace Omics.Fragmentation
 {
-    public struct Product
+    public class Product : IHasMass
     {
-        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,
-            int fragmentNumber, int aminoAcidPosition, double neutralLoss, ProductType? secondaryProductType = null, int secondaryFragmentNumber = 0)
+            int fragmentNumber, int residuePosition, double neutralLoss, ProductType? secondaryProductType = null,
+            int secondaryFragmentNumber = 0)
         {
             NeutralMass = neutralMass;
             ProductType = productType;
             NeutralLoss = neutralLoss;
             Terminus = terminus;
             FragmentNumber = fragmentNumber;
-            AminoAcidPosition = aminoAcidPosition;
+            ResiduePosition = residuePosition;
             SecondaryProductType = secondaryProductType;
             SecondaryFragmentNumber = secondaryFragmentNumber;
         }
@@ -70,29 +73,35 @@ public override string ToString()
         {
             if (SecondaryProductType == null)
             {
-                return ProductType + "" + FragmentNumber + ";" + NeutralMass.ToString("F5") + "-" + string.Format("{0:0.##}", NeutralLoss);
+                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);
+                return ProductType + "I" + SecondaryProductType.Value + "[" + FragmentNumber + "-" +
+                       SecondaryFragmentNumber + "]" + ";" + NeutralMass.ToString("F5") + "-" +
+                       string.Format("{0:0.##}", NeutralLoss);
             }
         }
 
         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(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/ProductType.cs → mzLib/Omics/Fragmentation/ProductType.cs

@@ -1,24 +1,22 @@
-using System.Collections.Generic;
-
-namespace Proteomics.Fragmentation
+namespace Omics.Fragmentation
 {
     public enum ProductType
     {
         //Ion Type      Neutral Mr
         //a             [N]+[M]-CHO
         //a*	        a-NH3
-        //a°	        a-H2O
+        //a°	        a-H2O
         //b             [N]+[M]-H
         //b*	        b-NH3
-        //b°	        b-H2O
+        //b°	        b-H2O
         //c             [N]+[M]+NH2
-        //d             a – partial side chain
-        //v             y – complete side chain
-        //w             z – partial side chain
+        //d             a – partial side chain
+        //v             y – complete side chain
+        //w             z – partial side chain
         //x             [C]+[M]+CO-H
         //y             [C]+[M]+H
         //y*	        y-NH3
-        //y°	        y-H2O
+        //y°	        y-H2O
         //z             [C]+[M]-NH2
 
         a,
@@ -40,5 +38,4 @@ public enum ProductType
         Ycore, //Glyco core Y ions // [pep] + Neutral core Glycan mass (such as: [pep] + [N]) //Which already consider the loss of H2O and H-transfer
         Y //Glyco Y ions // [pep] + other Glycan mass 
     }
-
-}
+}

mzLib/Omics/Omics.csproj

@@ -0,0 +1,15 @@
+<Project Sdk="Microsoft.NET.Sdk">
+
+  <PropertyGroup>
+    <TargetFramework>net6.0</TargetFramework>
+	<Platforms>x64</Platforms>
+    <ImplicitUsings>enable</ImplicitUsings>
+    <Nullable>enable</Nullable>
+  </PropertyGroup>
+
+  <ItemGroup>
+    <ProjectReference Include="..\Chemistry\Chemistry.csproj" />
+    <ProjectReference Include="..\MassSpectrometry\MassSpectrometry.csproj" />
+  </ItemGroup>
+
+</Project>

mzLib/Omics/SpectrumMatch/LibrarySpectrum.cs

@@ -0,0 +1,93 @@
+using System.Text;
+using Easy.Common.Extensions;
+using MassSpectrometry;
+using MassSpectrometry.MzSpectra;
+using Omics.Fragmentation;
+
+namespace Omics.SpectrumMatch
+{
+    public class LibrarySpectrum : MzSpectrum
+    {
+        public string Sequence { get; set; }
+        public double? RetentionTime { get; set; }
+        public double PrecursorMz { get; set; }
+        public int ChargeState { get; set; }
+        public List<MatchedFragmentIon> MatchedFragmentIons { get; set; }
+        public bool IsDecoy { get; set; }
+
+        public string Name
+        {
+            get { return Sequence + "/" + ChargeState; }
+        }
+
+        public LibrarySpectrum(string sequence, double precursorMz, int chargeState, List<MatchedFragmentIon> peaks, double? rt, bool isDecoy = false) : base(peaks.Select(p => p.Mz).ToArray(), peaks.Select(p => p.Intensity).ToArray(), false)
+        {
+            Sequence = sequence;
+            PrecursorMz = precursorMz;
+            MatchedFragmentIons = peaks;
+            ChargeState = chargeState;
+            IsDecoy = isDecoy;
+            RetentionTime = rt;
+            Array.Sort(XArray, YArray);
+        }
+
+        /// <summary>
+        /// This function enables the spectrum angle to be computed between an individual experimental spectrum and the loaded library spectrum within MetaDraw
+        /// </summary>
+        /// <param name="librarySpectrum"></param>
+        /// <returns></returns>
+        public string CalculateSpectralAngleOnTheFly(List<MatchedFragmentIon> spectrumMatchFragments)
+        {
+            if (!spectrumMatchFragments.Any())
+            {
+                return "N/A";
+            }
+
+            if (spectrumMatchFragments.IsNotNullOrEmpty()) { }
+            SpectralSimilarity spectraComparison = new SpectralSimilarity(
+                spectrumMatchFragments.Select(f => f.Mz).ToArray(),
+                spectrumMatchFragments.Select(f => f.Intensity).ToArray(),
+                MatchedFragmentIons.Select(f => f.Mz).ToArray(),
+                MatchedFragmentIons.Select(f => f.Intensity).ToArray(),
+                SpectralSimilarity.SpectrumNormalizationScheme.mostAbundantPeak,
+                toleranceInPpm: 20,
+                allPeaks: true);
+            double? spectralContrastAngle = spectraComparison.SpectralContrastAngle();
+
+            return spectralContrastAngle == null
+                ? "N/A"
+                : ((double)spectralContrastAngle).ToString("F4");
+        }
+
+        public override string ToString()
+        {
+            StringBuilder spectrum = new StringBuilder();
+            spectrum.Append("Name: " + Name);
+            spectrum.Append("\nMW: " + PrecursorMz);
+            spectrum.Append("\nComment: ");
+            spectrum.Append("Parent=" + PrecursorMz);
+            spectrum.Append(" RT=" + RetentionTime);
+            spectrum.Append("\nNum peaks: " + MatchedFragmentIons.Count);
+
+            double maxIntensity = MatchedFragmentIons.Select(b => b.Intensity).Max();
+
+            foreach (MatchedFragmentIon matchedIon in MatchedFragmentIons)
+            {
+                double intensityFraction = matchedIon.Intensity / maxIntensity;
+
+                string neutralLoss = null;
+                if (matchedIon.NeutralTheoreticalProduct.NeutralLoss != 0)
+                {
+                    neutralLoss = "-" + matchedIon.NeutralTheoreticalProduct.NeutralLoss;
+                }
+
+                spectrum.Append("\n" + matchedIon.Mz + "\t" + intensityFraction + "\t" + "\"" +
+                    matchedIon.NeutralTheoreticalProduct.ProductType.ToString() +
+                    matchedIon.NeutralTheoreticalProduct.FragmentNumber.ToString() + "^" +
+                    matchedIon.Charge + neutralLoss + "/" + 0 + "ppm" + "\"");
+            }
+
+            return spectrum.ToString();
+        }
+    }
+}