Small fixes

Author: caetera

Writer/MetadataWriter.cs

@@ -4,7 +4,6 @@
 using System.IO;
 using System.Linq;
 using System.Reflection;
-using System.Web.WebSockets;
 using log4net;
 using Newtonsoft.Json;
 using ThermoFisher.CommonCore.Data;
@@ -122,16 +121,14 @@ public void WriteMetadata(IRawDataPlus rawFile, int firstScanNumber, int lastSca
             switch (_parseInput.MetadataFormat)
             {
                 case MetadataFormat.JSON:
-                    _metadataFileName = _parseInput.MetadataOutputFile != null
-                        ? _parseInput.MetadataOutputFile
-                        : Path.Combine(_parseInput.OutputDirectory, _parseInput.RawFileNameWithoutExtension) +
+                    _metadataFileName = _parseInput.MetadataOutputFile ?? 
+                        Path.Combine(_parseInput.OutputDirectory, _parseInput.RawFileNameWithoutExtension) +
                           "-metadata.json";
                     WriteJsonMetada(rawFile, firstScanNumber, lastScanNumber);
                     break;
                 case MetadataFormat.TXT:
-                    _metadataFileName = _parseInput.MetadataOutputFile != null
-                        ? _parseInput.MetadataOutputFile
-                        : Path.Combine(_parseInput.OutputDirectory, _parseInput.RawFileNameWithoutExtension) +
+                    _metadataFileName = _parseInput.MetadataOutputFile ??
+                        Path.Combine(_parseInput.OutputDirectory, _parseInput.RawFileNameWithoutExtension) +
                           "-metadata.txt";
                     WriteTextMetadata(rawFile, firstScanNumber, lastScanNumber);
                     break;
@@ -371,7 +368,6 @@ private void WriteTextMetadata(IRawDataPlus rawFile, int firstScanNumber, int la
                     output.Add("Firmware version=" + rawFile.GetInstrumentData().HardwareVersion);
                 }
 
-
                 // MS Data
                 output.Add("#MsData");
                 foreach (KeyValuePair<string, int> entry in msTypes)

Writer/MgfSpectrumWriter.cs

@@ -5,11 +5,9 @@
 using System.Reflection;
 using System.Text.RegularExpressions;
 using log4net;
-using ThermoFisher.CommonCore.Data;
 using ThermoFisher.CommonCore.Data.Business;
 using ThermoFisher.CommonCore.Data.FilterEnums;
 using ThermoFisher.CommonCore.Data.Interfaces;
-using ThermoRawFileParser.Util;
 
 namespace ThermoRawFileParser.Writer
 {

Writer/MzMlSpectrumWriter.cs

@@ -1,8 +1,6 @@
 using System;
 using System.Collections.Generic;
 using System.Collections.Specialized;
-using System.Diagnostics;
-using System.Diagnostics.Eventing.Reader;
 using System.Globalization;
 using System.IO;
 using System.IO.Compression;
@@ -527,7 +525,7 @@ public override void Write(IRawDataPlus rawFile, int firstScanNumber, int lastSc
                 _writer.WriteEndElement(); // spectrumList                                                
 
                 index = 0;
-                var chromatograms = ConstructChromatograms(firstScanNumber, lastScanNumber);
+                var chromatograms = ConstructChromatograms();
                 if (!chromatograms.IsNullOrEmpty())
                 {
                     // ChromatogramList
@@ -914,7 +912,7 @@ private void Serialize<T>(XmlSerializer serializer, T t)
         /// <param name="firstScanNumber">the first scan number</param>
         /// <param name="lastScanNumber">the last scan number</param>
         /// <returns>a list of chromatograms</returns>
-        private List<ChromatogramType> ConstructChromatograms(int firstScanNumber, int lastScanNumber)
+        private List<ChromatogramType> ConstructChromatograms()
         {
             var chromatograms = new List<ChromatogramType>();
 
@@ -2470,15 +2468,14 @@ private PrecursorListType ConstructPrecursorList(int precursorScanNumber, IScanE
                 var SPSPrecursor = new PrecursorType
                 {
                     selectedIonList =
-                        new SelectedIonListType {count = "1", selectedIon = new ParamGroupType[1]},
-                    spectrumRef = spectrumRef
-                };
-
-                //Isolation window for SPS masses is the same as for the first precursor
-                SPSPrecursor.isolationWindow =
+                        new SelectedIonListType { count = "1", selectedIon = new ParamGroupType[1] },
+                    spectrumRef = spectrumRef,
+                    //Isolation window for SPS masses is the same as for the first precursor
+                    isolationWindow =
                 new ParamGroupType
                 {
                     cvParam = new CVParamType[3]
+                }
                 };
 
                 SPSPrecursor.isolationWindow.cvParam[0] =
@@ -2755,14 +2752,13 @@ private ScanListType ConstructScanList(int scanNumber, Scan scan)
 
             var scanType = new ScanType
             {
-                cvParam = scanTypeCvParams.ToArray()
-            };
-
-            // Scan window list
-            scanType.scanWindowList = new ScanWindowListType
-            {
-                count = 1,
-                scanWindow = new ParamGroupType[1]
+                cvParam = scanTypeCvParams.ToArray(),
+                // Scan window list
+                scanWindowList = new ScanWindowListType
+                {
+                    count = 1,
+                    scanWindow = new ParamGroupType[1]
+                }
             };
             var scanWindow = new ParamGroupType
             {
@@ -2853,22 +2849,6 @@ private static byte[] GetZLib64BitArray(ICollection<double> array)
             return bytes;
         }
 
-        /// <summary>
-        /// Calculate the RAW file checksum
-        /// </summary>
-        /// <returns>the checksum string</returns>
-        private string CalculateMD5Checksum()
-        {
-            using (var md5 = MD5.Create())
-            {
-                using (var stream = File.OpenRead(ParseInput.RawFilePath))
-                {
-                    var hash = md5.ComputeHash(stream);
-                    return BitConverter.ToString(hash).Replace("-", "").ToLowerInvariant();
-                }
-            }
-        }
-
         /// <summary>
         /// Calculate the RAW file checksum
         /// </summary>

Writer/SpectrumWriter.cs

@@ -107,7 +107,7 @@ private string NormalizeFileName(string outputFile, string extension, bool gzip)
             string tail = "";
 
             string[] extensions;
-            if (ParseInput.Gzip)
+            if (gzip)
                 extensions = new string[] { ".gz", extension };
             else
                 extensions = new string[] { extension };