trailerData class

Author: caetera

ThermoRawFileParser.csproj

@@ -155,6 +155,7 @@
     <Compile Include="RawFileParser.cs" />
     <Compile Include="Util\LimitedSizeDictionary.cs" />
     <Compile Include="Util\Peptide.cs" />
+    <Compile Include="Writer\ScanTrailer.cs" />
     <Compile Include="XIC\JSONInputUnit.cs" />
     <Compile Include="XIC\JSONParser.cs" />
     <Compile Include="XIC\XicData.cs" />

Writer/MzMlSpectrumWriter.cs

@@ -1142,12 +1142,37 @@ private SpectrumType ConstructMSSpectrum(int scanNumber)
             };
 
             // Trailer extra data list
-            var trailerData = _rawFile.GetTrailerExtraInformation(scanNumber);
+            var trailerData = new ScanTrailer(_rawFile.GetTrailerExtraInformation(scanNumber));
             int? charge = null;
             double? monoisotopicMz = null;
             double? ionInjectionTime = null;
             double? FAIMSCV = null;
             List<double> SPSMasses = new List<double>();
+
+            charge = trailerData.AsPositiveInt("Charge State:");
+            monoisotopicMz = trailerData.AsDouble("Monoisotopic M/Z:");
+            ionInjectionTime = trailerData.AsDouble("Ion Injection Time (ms):");
+            if (trailerData.AsBool("FAIMS Voltage On:").GetValueOrDefault(false))
+                FAIMSCV = trailerData.AsDouble("FAIMS CV:");
+
+            //tune version < 3 produced trailer entry like "SPS Mass #", one entry per mass
+            foreach (var label in trailerData.MatchKeys(SPSentry))
+            {
+                var mass = trailerData.AsDouble(label).GetValueOrDefault(0);
+                if (mass > 0) SPSMasses.Add((double)mass); //zero means mass does not exist
+            }
+
+            //tune version == 3 produces trailer entry "SPS Masses", comma separated list of masses 
+            foreach (var label in trailerData.MatchKeys(SPSentry3))
+            {
+                foreach (var mass in trailerData.Get(label).Trim().Split(new char[] { ',' }, StringSplitOptions.RemoveEmptyEntries))
+                {
+                    SPSMasses.Add(double.Parse(mass));
+                }
+
+            }
+
+            /*var trailerData = _rawFile.GetTrailerExtraInformation(scanNumber);
             for (var i = 0; i < trailerData.Length; i++)
             {
                 if (trailerData.Labels[i] == "Charge State:")
@@ -1192,13 +1217,15 @@ private SpectrumType ConstructMSSpectrum(int scanNumber)
                     }
                     
                 }
-            }
+            }*/
 
             // Construct and set the scan list element of the spectrum
             var scanListType = ConstructScanList(scanNumber, scan, scanFilter, scanEvent, monoisotopicMz,
                 ionInjectionTime);
             spectrum.scanList = scanListType;
 
+            int? trailerMasterScan;
+
             switch (scanFilter.MSOrder)
             {
                 case MSOrderType.Ms:
@@ -1211,7 +1238,8 @@ private SpectrumType ConstructMSSpectrum(int scanNumber)
                     });
 
                     // Keep track of scan number for precursor reference
-                    _precursorMs1ScanNumber = scanNumber;
+                    trailerMasterScan = trailerData.AsInt("Master Scan Number:");
+                    _precursorMs1ScanNumber = trailerMasterScan.HasValue ? trailerMasterScan.Value : scanNumber;
 
                     break;
                 case MSOrderType.Ms2:
@@ -1232,7 +1260,9 @@ private SpectrumType ConstructMSSpectrum(int scanNumber)
                             _precursorMs2ScanNumbers.Remove(result.Groups[1].Value);
                         }
 
-                        _precursorMs2ScanNumbers.Add(result.Groups[1].Value, scanNumber);
+                        trailerMasterScan = trailerData.AsInt("Master Scan Number:");
+                        _precursorMs2ScanNumbers.Add(result.Groups[1].Value,
+                            trailerMasterScan.HasValue ? trailerMasterScan.Value : scanNumber);
                     }
 
                     // Construct and set the precursor list element of the spectrum                    

Writer/ScanTrailer.cs

@@ -0,0 +1,107 @@
+using System;
+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
+{
+    public class ScanTrailer
+    {
+        public int Length { get => data.Count; }
+
+        public string[] Labels { get => data.Keys.ToArray(); }
+
+        public string[] Values { get => data.Values.ToArray(); }
+
+        private Dictionary<string, string> data;
+
+        public ScanTrailer(LogEntry trailerData)
+        {
+            data = new Dictionary<string, string>();
+
+            for (int i = 0; i < trailerData.Length; i++)
+            {
+                data[trailerData.Labels[i]] = trailerData.Values[i].Trim();
+            }
+        }
+
+        public bool? AsBool(string key)
+        {
+            if(data.ContainsKey(key))
+            {
+                var stringValue = data[key].ToLower();
+
+                switch (stringValue)
+                {
+                    case "on":
+                    case "true":
+                    case "yes":
+                        return true;
+                    default:
+                        return false;
+                }
+            }
+
+            return null;
+        }
+
+        public double? AsDouble(string key)
+        {
+            if (data.ContainsKey(key))
+            {
+                if (double.TryParse(data[key], out var result)) return result;
+            }
+            return null;
+        }
+
+        public int? AsInt(string key)
+        {
+            if (data.ContainsKey(key))
+            {
+                if (int.TryParse(data[key], out var result)) return result;
+            }
+            return null;
+        }
+
+        public int? AsPositiveInt(string key)
+        {
+            int? value = AsInt(key);
+
+            if (value != null && value > 0) return value;
+            else return null;
+
+        }
+
+        public string AsString(string key)
+        {
+            return Get(key);
+        }
+
+        public string Get(string key)
+        {
+            if (data.ContainsKey(key))
+            {
+                return data[key];
+            }
+            return null;
+        }
+
+        public bool Has(string key)
+        {
+            return data.ContainsKey(key);
+        }
+
+        public IEnumerable<string> MatchKeys(Regex regex)
+        {
+            return data.Keys.Where(k => regex.IsMatch(k));
+        }
+
+        public IEnumerable<string> MatchValues(Regex regex)
+        {
+            return data.Where(item => regex.IsMatch(item.Key)).Select(item => item.Value);
+        }
+    }
+}