Analyte type

MetaMorpheus/EngineLayer/AnalyteType.cs

@@ -0,0 +1,56 @@
+using System.Collections.Generic;
+
+namespace EngineLayer
+{
+    public enum AnalyteType
+    {
+        Peptide,
+        Proteoform,
+        Oligo
+    }
+
+    /// <summary>
+    /// Accessor methods for specific information about certain analyte types
+    /// </summary>
+    public static class AnalyteTypeExtensions
+    {
+        private static readonly Dictionary<AnalyteType, AnalyteTypeData> AnalyteTypes = new()
+            {
+                { AnalyteType.Peptide, new AnalyteTypeData("PSM", "Peptide", "Protein", "psmtsv") },
+                { AnalyteType.Proteoform, new AnalyteTypeData("PSM", "Proteoform", "Protein", "psmtsv") },
+                { AnalyteType.Oligo, new AnalyteTypeData("OSM", "Oligo", "Transcript", "osmtsv") },
+            };
+
+        public static string GetSpectralMatchLabel(this AnalyteType analyteType) => AnalyteTypes[analyteType].SpectralMatchLabel;
+        public static string GetSpectralMatchExtension(this AnalyteType analyteType) => AnalyteTypes[analyteType].SpectralMatchExtension;
+        public static string GetUniqueFormLabel(this AnalyteType analyteType) => AnalyteTypes[analyteType].UniqueFormLabel;
+        public static string GetBioPolymerLabel(this AnalyteType analyteType) => AnalyteTypes[analyteType].BioPolymerLabel;
+    }
+
+    /// <summary>
+    /// Represents an analyte type and is used to determine the output format of the analyte type.
+    /// </summary>
+    internal class AnalyteTypeData(string spectralMatchLabel, string uniqueFormLabel, string bioPolymerLabel, string spectralMatchExtension)
+    {
+        /// <summary>
+        /// Gets or sets the label for spectral matches (e.g. PSM).
+        /// </summary>
+        internal string SpectralMatchLabel { get; init; } = spectralMatchLabel;
+
+        /// <summary>
+        /// Extension for spectral matches (e.g. psmtsv).
+        /// </summary>
+        internal string SpectralMatchExtension { get; init; } = spectralMatchExtension;
+
+        /// <summary>
+        /// Gets or sets the label for unique forms (e.g. Peptide).
+        /// </summary>
+        internal string UniqueFormLabel { get; init; } = uniqueFormLabel;
+
+        /// <summary>
+        /// Gets or sets the label for grouped forms (e.g. Protein).
+        /// </summary>
+        internal string BioPolymerLabel { get; init; } = bioPolymerLabel;
+    }
+}
+

MetaMorpheus/EngineLayer/GlobalVariables.cs

@@ -34,7 +34,7 @@ public static class GlobalVariables
         private static char[] _InvalidAminoAcids;
 
         // this affects output labels, etc. and can be changed to "Proteoform" for top-down searches
-        public static string AnalyteType;
+        public static AnalyteType AnalyteType;
 
         public static List<string> ErrorsReadingMods;
 
@@ -65,7 +65,7 @@ public static void SetUpGlobalVariables()
             Loaders.LoadElements();
             AcceptedDatabaseFormats = new List<string> { ".fasta", ".fa", ".xml", ".msp" };
             AcceptedSpectraFormats = new List<string> { ".raw", ".mzml", ".mgf" };
-            AnalyteType = "Peptide";
+            AnalyteType = AnalyteType.Peptide;
             _InvalidAminoAcids = new char[] { 'X', 'B', 'J', 'Z', ':', '|', ';', '[', ']', '{', '}', '(', ')', '+', '-' };
             ExperimentalDesignFileName = "ExperimentalDesign.tsv";
             SeparationTypes = new List<string> { { "HPLC" }, { "CZE" } };

MetaMorpheus/MetaMorpheus.sln.DotSettings

@@ -1,4 +1,5 @@
 <wpf:ResourceDictionary xml:space="preserve" xmlns:x="http://schemas.microsoft.com/winfx/2006/xaml" xmlns:s="clr-namespace:System;assembly=mscorlib" xmlns:ss="urn:shemas-jetbrains-com:settings-storage-xaml" xmlns:wpf="http://schemas.microsoft.com/winfx/2006/xaml/presentation">
+	<s:Boolean x:Key="/Default/UserDictionary/Words/=Analyte/@EntryIndexedValue">True</s:Boolean>
 	<s:Boolean x:Key="/Default/UserDictionary/Words/=Calib/@EntryIndexedValue">True</s:Boolean>
 	<s:Boolean x:Key="/Default/UserDictionary/Words/=coisolation/@EntryIndexedValue">True</s:Boolean>
 	<s:Boolean x:Key="/Default/UserDictionary/Words/=crosslinked/@EntryIndexedValue">True</s:Boolean>
@@ -20,9 +21,11 @@
 	<s:Boolean x:Key="/Default/UserDictionary/Words/=Nterm/@EntryIndexedValue">True</s:Boolean>
 	<s:Boolean x:Key="/Default/UserDictionary/Words/=Ogly/@EntryIndexedValue">True</s:Boolean>
 	<s:Boolean x:Key="/Default/UserDictionary/Words/=oglyco/@EntryIndexedValue">True</s:Boolean>
+	<s:Boolean x:Key="/Default/UserDictionary/Words/=Oligo/@EntryIndexedValue">True</s:Boolean>
 	<s:Boolean x:Key="/Default/UserDictionary/Words/=Phospho/@EntryIndexedValue">True</s:Boolean>
 	<s:Boolean x:Key="/Default/UserDictionary/Words/=prot/@EntryIndexedValue">True</s:Boolean>
 	<s:Boolean x:Key="/Default/UserDictionary/Words/=proteingroup/@EntryIndexedValue">True</s:Boolean>
+	<s:Boolean x:Key="/Default/UserDictionary/Words/=Proteoform/@EntryIndexedValue">True</s:Boolean>
 	<s:Boolean x:Key="/Default/UserDictionary/Words/=psmtsv/@EntryIndexedValue">True</s:Boolean>
 	<s:Boolean x:Key="/Default/UserDictionary/Words/=pwsm/@EntryIndexedValue">True</s:Boolean>
 	<s:Boolean x:Key="/Default/UserDictionary/Words/=Silac/@EntryIndexedValue">True</s:Boolean>

MetaMorpheus/TaskLayer/MetaMorpheusTask.cs

@@ -1143,11 +1143,11 @@ public static void DetermineAnalyteType(CommonParameters commonParameters)
                 && commonParameters.DigestionParams.Protease != null
                 && commonParameters.DigestionParams.Protease.Name == "top-down")
             {
-                GlobalVariables.AnalyteType = "Proteoform";
+                GlobalVariables.AnalyteType = AnalyteType.Proteoform;
             }
             else
             {
-                GlobalVariables.AnalyteType = "Peptide";
+                GlobalVariables.AnalyteType = AnalyteType.Peptide;
             }
         }