Use trailer precursor scan if possible + docstrings for ScanTrailer

Author: caetera

Writer/MzMlSpectrumWriter.cs

@@ -1170,9 +1170,9 @@ private SpectrumType ConstructMSSpectrum(int scanNumber)
             //tune version == 3
             if (trailerData.Has("SPS Masses:"))
             {
-                foreach (var label in trailerData.MatchKeys(SPSentry3))
+                foreach (var labelvalue in trailerData.MatchValues(SPSentry3))
                 {
-                    foreach (var mass in trailerData.Get(label).Trim().Split(new char[] { ',' }, StringSplitOptions.RemoveEmptyEntries))
+                    foreach (var mass in labelvalue.Trim().Split(new char[] { ',' }, StringSplitOptions.RemoveEmptyEntries))
                     {
                         SPSMasses.Add(double.Parse(mass));
                     }
@@ -1270,6 +1270,10 @@ private SpectrumType ConstructMSSpectrum(int scanNumber)
                         value = ""
                     });
 
+                    //update precursor scan if it is provided in trailer data
+                    var trailerMasterScan = trailerData.AsPositiveInt("Master Scan Number:");
+                    if (trailerMasterScan.HasValue) _precursorMs1ScanNumber = trailerMasterScan.Value;
+
                     // Keep track of scan number and isolation m/z for precursor reference                   
                     var result = FilterStringIsolationMzPattern.Match(scanEvent.ToString());
                     if (result.Success)

Writer/ScanTrailer.cs

@@ -1,9 +1,6 @@
-using System;
-using System.Collections.Generic;
+using System.Collections.Generic;
 using System.Linq;
-using System.Text;
 using System.Text.RegularExpressions;
-using System.Threading.Tasks;
 using ThermoFisher.CommonCore.Data.Business;
 
 namespace ThermoRawFileParser.Writer
@@ -16,7 +13,7 @@ public class ScanTrailer
 
         public string[] Values { get => data.Values.ToArray(); }
 
-        private Dictionary<string, string> data;
+        private readonly Dictionary<string, string> data;
 
         public ScanTrailer(LogEntry trailerData)
         {
@@ -28,6 +25,11 @@ public ScanTrailer(LogEntry trailerData)
             }
         }
 
+        /// <summary>
+        /// Try returning selected trailer element as boolean value,
+        /// if the element does not exist or cannot be converted to boolean return null
+        /// </summary>
+        /// <param name="key">name of the element</param>
         public bool? AsBool(string key)
         {
             if(data.ContainsKey(key))
@@ -48,6 +50,11 @@ public ScanTrailer(LogEntry trailerData)
             return null;
         }
 
+        /// <summary>
+        /// Try returning selected trailer element as double value,
+        /// if the element does not exist or cannot be converted to double return null
+        /// </summary>
+        /// <param name="key">name of the element</param>
         public double? AsDouble(string key)
         {
             if (data.ContainsKey(key))
@@ -57,6 +64,11 @@ public ScanTrailer(LogEntry trailerData)
             return null;
         }
 
+        /// <summary>
+        /// Try returning selected trailer element as integer value,
+        /// if the element does not exist or cannot be converted to integer return null
+        /// </summary>
+        /// <param name="key">name of the element</param>
         public int? AsInt(string key)
         {
             if (data.ContainsKey(key))
@@ -66,6 +78,11 @@ public ScanTrailer(LogEntry trailerData)
             return null;
         }
 
+        /// <summary>
+        /// Try returning selected trailer element as strictly positive (non zero) integer value,
+        /// if the element does not exist or cannot be converted to strictly positive integer return null
+        /// </summary>
+        /// <param name="key">name of the element</param>
         public int? AsPositiveInt(string key)
         {
             int? value = AsInt(key);
@@ -75,11 +92,21 @@ public ScanTrailer(LogEntry trailerData)
 
         }
 
+        /// <summary>
+        /// Try returning selected trailer element as string,
+        /// alias to `Get`
+        /// </summary>
+        /// <param name="key">name of the element</param>
         public string AsString(string key)
         {
             return Get(key);
         }
 
+        /// <summary>
+        /// Try getting selected trailer element by name,
+        /// if the element does not exist return null
+        /// </summary>
+        /// <param name="key">name of the element</param>
         public string Get(string key)
         {
             if (data.ContainsKey(key))
@@ -89,16 +116,28 @@ public string Get(string key)
             return null;
         }
 
+        /// <summary>
+        /// Check if selected trailer element exists
+        /// </summary>
+        /// <param name="key">name of the element</param>
         public bool Has(string key)
         {
             return data.ContainsKey(key);
         }
 
+        /// <summary>
+        /// Return iterator over trailer element names matching regex
+        /// </summary>
+        /// <param name="regex">compiled regex object</param>
         public IEnumerable<string> MatchKeys(Regex regex)
         {
             return data.Keys.Where(k => regex.IsMatch(k));
         }
 
+        /// <summary>
+        /// Return iterator over trailer element values which names are matching regex
+        /// </summary>
+        /// <param name="regex">compiled regex object</param>
         public IEnumerable<string> MatchValues(Regex regex)
         {
             return data.Where(item => regex.IsMatch(item.Key)).Select(item => item.Value);