Advanced MSLevel filter

Author: caetera

MainClass.cs

@@ -766,6 +766,8 @@ private static void RegularParametersParsing(string[] args)
                     if (parseInput.OutputFormat == OutputFormat.IndexMzML) parseInput.OutputFormat = OutputFormat.MzML;
                 }
 
+                parseInput.MaxLevel = parseInput.MsLevel.Max();
+
                 if (parseInput.S3Url != null && parseInput.S3AccessKeyId != null &&
                     parseInput.S3SecretAccessKey != null && parseInput.BucketName != null)
                     if (Uri.IsWellFormedUriString(parseInput.S3Url, UriKind.Absolute))

ParseInput.cs

@@ -96,6 +96,8 @@ public int Warnings
 
         public HashSet<int> MsLevel { get; set; }
 
+        public int MaxLevel { get; set; }
+
         public bool MgfPrecursor { get; set; }
 
         public bool NoiseData { get; set; }
@@ -136,6 +138,7 @@ public ParseInput()
             Vigilant = false;
             _errors = 0;
             _warnings = 0;
+            MaxLevel = 10;
         }
 
         public ParseInput(string rawFilePath, string rawDirectoryPath, string outputDirectory, OutputFormat outputFormat

Writer/MzMlSpectrumWriter.cs

@@ -401,20 +401,23 @@ public override void Write(IRawDataPlus rawFile, int firstScanNumber, int lastSc
 
 
                         SpectrumType spectrum = null;
+                        int level;
 
                         try
                         {
-                            spectrum = ConstructMSSpectrum(scanNumber);
+                            level = (int) _rawFile.GetScanEventForScanNumber(scanNumber).MSOrder; //applying MS level pre filter
+                            if (level <= ParseInput.MaxLevel)
+                                spectrum = ConstructMSSpectrum(scanNumber);
                         }
                         catch (Exception ex)
                         {
                             Log.Error($"Scan #{scanNumber} cannot be processed because of the following exception: {ex.Message}\n{ex.StackTrace}");
                             ParseInput.NewError();
                         }
 
-                        var level = spectrum != null ? int.Parse(spectrum.cvParam.Where(p => p.accession == "MS:1000511").First().value) : 0;
+                        level = spectrum != null ? int.Parse(spectrum.cvParam.Where(p => p.accession == "MS:1000511").First().value) : 0;
 
-                        if (spectrum != null && ParseInput.MsLevel.Contains(level)) //applying MS level filter
+                        if (spectrum != null && ParseInput.MsLevel.Contains(level)) //applying final MS filter
                         {
                             spectrum.index = index.ToString();
                             if (_doIndexing)