minor changes before release

compomics · Apr 1, 2021 · f2c707e · f2c707e
1 parent 3265f38
commit f2c707e
Show file tree

Hide file tree

Showing 5 changed files with 35 additions and 54 deletions.
diff --git a/ParseInput.cs b/ParseInput.cs
@@ -29,9 +29,6 @@ public string RawFilePath
                 if (value != null)
                 {
                     RawFileNameWithoutExtension = Path.GetFileNameWithoutExtension(value);
-                    //do we need it?
-                    var splittedPath = value.Split('/');
-                    _rawFileName = splittedPath[splittedPath.Length - 1];
                 }
             }
         }
@@ -94,12 +91,6 @@ public string RawFilePath
 
         public string BucketName { get; set; }
 
-        //this property assigned but never used
-        /// <summary>
-        /// The raw file name.
-        /// </summary>
-        private string _rawFileName;
-
         /// <summary>
         /// The RAW file name without extension.
         /// </summary>

diff --git a/ThermoRawFileParserTest/packages.config b/ThermoRawFileParserTest/packages.config
@@ -14,4 +14,6 @@
   <package id="NUnit" version="3.13.1" targetFramework="net472" />
   <package id="PSI_Interface" version="2.3.2" targetFramework="net472" />
   <package id="zlib.net" version="1.0.4.0" targetFramework="net471" />
-</packages>
+  <package id="ThermoFisher.CommonCore.Data" version="5.0.0.71" targetFramework="net472" />
+  <package id="ThermoFisher.CommonCore.RawFileReader" version="5.0.0.71" targetFramework="net472" />
+</packages>
diff --git a/Writer/MgfSpectrumWriter.cs b/Writer/MgfSpectrumWriter.cs
@@ -108,32 +108,11 @@ public override void Write(IRawDataPlus rawFile, int firstScanNumber, int lastSc
                             $"RTINSECONDS={(retentionTime * 60).ToString(CultureInfo.InvariantCulture)}");
 
                         // Trailer extra data list
-                        var trailerData = rawFile.GetTrailerExtraInformation(scanNumber);
-                        int? charge = null;
-                        double? monoisotopicMz = null;
-                        double? isolationWidth = null;
-                        for (var i = 0; i < trailerData.Length; i++)
-                        {
-                            if (trailerData.Labels[i] == "Charge State:")
-                            {
-                                if (Convert.ToInt32(trailerData.Values[i]) > 0)
-                                {
-                                    charge = Convert.ToInt32(trailerData.Values[i]);
-                                }
-                            }
-
-                            if (trailerData.Labels[i] == "Monoisotopic M/Z:")
-                            {
-                                monoisotopicMz = double.Parse(trailerData.Values[i], NumberStyles.Any,
-                                    CultureInfo.CurrentCulture);
-                            }
-
-                            if (trailerData.Labels[i] == "MS" + (int) scanFilter.MSOrder + " Isolation Width:")
-                            {
-                                isolationWidth = double.Parse(trailerData.Values[i], NumberStyles.Any,
-                                    CultureInfo.CurrentCulture);
-                            }
-                        }
+                        var trailerData = new ScanTrailer(rawFile.GetTrailerExtraInformation(scanNumber));
+                        int? charge = trailerData.AsPositiveInt("Charge State:");
+                        double? monoisotopicMz = trailerData.AsDouble("Monoisotopic M/Z:");
+                        double? isolationWidth =
+                            trailerData.AsDouble("MS" + (int) scanFilter.MSOrder + " Isolation Width:");
 
                         if (reaction != null)
                         {
@@ -261,7 +240,7 @@ private string ConstructPrecursorReference(MSOrderType msOrder, int scanNumber,
 
                     break;
             }
-            
+
             return precursorReference;
         }
     }

diff --git a/Writer/MzMlSpectrumWriter.cs b/Writer/MzMlSpectrumWriter.cs
@@ -1164,20 +1164,16 @@ private SpectrumType ConstructMSSpectrum(int scanNumber)
 
             // Trailer extra data list
             var trailerData = new ScanTrailer(_rawFile.GetTrailerExtraInformation(scanNumber));
-            int? charge;
-            double? monoisotopicMz;
-            double? ionInjectionTime;
-            double? isolationWidth;
-            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):");
-            isolationWidth = trailerData.AsDouble("MS" + (int)scanFilter.MSOrder + " Isolation Width:");
+            int? charge = trailerData.AsPositiveInt("Charge State:");
+            double? monoisotopicMz = trailerData.AsDouble("Monoisotopic M/Z:");
+            double? ionInjectionTime = trailerData.AsDouble("Ion Injection Time (ms):");
+            double? isolationWidth = trailerData.AsDouble("MS" + (int)scanFilter.MSOrder + " Isolation Width:");
+            double? FAIMSCV = null;
             if (trailerData.AsBool("FAIMS Voltage On:").GetValueOrDefault(false))
                 FAIMSCV = trailerData.AsDouble("FAIMS CV:");
 
+            List<double> SPSMasses = new List<double>();
             //tune version < 3
             if (trailerData.Has("SPS Mass 1:"))
             {

diff --git a/Writer/ScanTrailer.cs b/Writer/ScanTrailer.cs
@@ -1,4 +1,5 @@
 using System.Collections.Generic;
+using System.Globalization;
 using System.Linq;
 using System.Text.RegularExpressions;
 using ThermoFisher.CommonCore.Data.Business;
@@ -7,11 +8,20 @@ namespace ThermoRawFileParser.Writer
 {
     public class ScanTrailer
     {
-        public int Length { get => data.Count; }
+        public int Length
+        {
+            get => data.Count;
+        }
 
-        public string[] Labels { get => data.Keys.ToArray(); }
+        public string[] Labels
+        {
+            get => data.Keys.ToArray();
+        }
 
-        public string[] Values { get => data.Values.ToArray(); }
+        public string[] Values
+        {
+            get => data.Values.ToArray();
+        }
 
         private readonly Dictionary<string, string> data;
 
@@ -32,7 +42,7 @@ public ScanTrailer(LogEntry trailerData)
         /// <param name="key">name of the element</param>
         public bool? AsBool(string key)
         {
-            if(data.ContainsKey(key))
+            if (data.ContainsKey(key))
             {
                 var stringValue = data[key].ToLower();
 
@@ -59,8 +69,10 @@ public ScanTrailer(LogEntry trailerData)
         {
             if (data.ContainsKey(key))
             {
-                if (double.TryParse(data[key], out var result)) return result;
+                if (double.TryParse(data[key], NumberStyles.Any,
+                    CultureInfo.CurrentCulture, out var result)) return result;
             }
+
             return null;
         }
 
@@ -75,6 +87,7 @@ public ScanTrailer(LogEntry trailerData)
             {
                 if (int.TryParse(data[key], out var result)) return result;
             }
+
             return null;
         }
 
@@ -89,7 +102,6 @@ public ScanTrailer(LogEntry trailerData)
 
             if (value != null && value > 0) return value;
             else return null;
-
         }
 
         /// <summary>
@@ -113,6 +125,7 @@ public string Get(string key)
             {
                 return data[key];
             }
+
             return null;
         }
 
@@ -143,4 +156,4 @@ public IEnumerable<string> MatchValues(Regex regex)
             return data.Where(item => regex.IsMatch(item.Key)).Select(item => item.Value);
         }
     }
-}
+}