PeakPicking with levels

Author: caetera

MainClass.cs

@@ -19,7 +19,7 @@ public static class MainClass
         private static readonly ILog Log =
             LogManager.GetLogger(System.Reflection.MethodBase.GetCurrentMethod().DeclaringType);
 
-        public const string Version = "1.3.3";
+        public const string Version = "1.4.0";
 
         public static void Main(string[] args)
         {
@@ -407,9 +407,9 @@ private static void RegularParametersParsing(string[] args)
                     v => parseInput.Gzip = v != null
                 },
                 {
-                    "p|noPeakPicking",
-                    "Don't use the peak picking provided by the native Thermo library. By default peak picking is enabled.",
-                    v => parseInput.NoPeakPicking = v != null
+                    "p:|noPeakPicking:",
+                    "Don't use the peak picking provided by the native Thermo library. By default peak picking is enabled. Optional argument allows disabling peak peaking only for selected MS levels and should be a comma-separated list of integers (1,2,3) and/or intervals (1-3), open-end intervals (1-) are allowed",
+                    v => parseInput.NoPeakPicking = v is null? ParseInput.AllLevels: ParseMsLevel(v)
                 },
                 {
                     "z|noZlibCompression",

ParseInput.cs

@@ -1,5 +1,4 @@
-using System;
-using System.Collections.Generic;
+using System.Collections.Generic;
 using System.IO;
 using ThermoRawFileParser.Writer;
 
@@ -8,7 +7,7 @@ namespace ThermoRawFileParser
     public class ParseInput
     {
         // All MS levels
-        private readonly HashSet<int> _allLevels = new HashSet<int>(new int[] {1, 2, 3, 4, 5, 6, 7, 8, 9, 10});
+        public static HashSet<int> AllLevels { get => new HashSet<int> { 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 }; }
 
         /// <summary>
         /// The RAW file path.
@@ -63,7 +62,7 @@ public string RawFilePath
         /// </summary>
         public bool Gzip { get; set; }
 
-        public bool NoPeakPicking { get; set; }
+        public HashSet<int> NoPeakPicking { get; set; }
 
         public bool NoZlibCompression { get; set; }
 
@@ -101,12 +100,12 @@ public ParseInput()
             MetadataFormat = MetadataFormat.NONE;
             OutputFormat = OutputFormat.NONE;
             Gzip = false;
-            NoPeakPicking = false;
+            NoPeakPicking = new HashSet<int>();
             NoZlibCompression = false;
             LogFormat = LogFormat.DEFAULT;
             IgnoreInstrumentErrors = false;
             AllDetectors = false;
-            MsLevel = _allLevels;
+            MsLevel = AllLevels;
             MgfPrecursor = false;
             StdOut = false;
         }

ThermoRawFileParserTest/WriterTests.cs

@@ -90,7 +90,7 @@ public void TestProfileMzml()
             var testRawFile = Path.Combine(AppDomain.CurrentDomain.BaseDirectory, @"Data/small.RAW");
             var parseInput = new ParseInput(testRawFile, null, tempFilePath, OutputFormat.MzML);
 
-            parseInput.NoPeakPicking = true;
+            parseInput.NoPeakPicking = new HashSet<int> { 1, 2 };
 
             RawFileParser.Parse(parseInput);
 

Writer/MgfSpectrumWriter.cs

@@ -139,7 +139,7 @@ public override void Write(IRawDataPlus rawFile, int firstScanNumber, int lastSc
                         // Write the filter string
                         //Writer.WriteLine($"SCANEVENT={scanEvent.ToString()}");
 
-                        if (!ParseInput.NoPeakPicking)
+                        if (!ParseInput.NoPeakPicking.Contains((int)scanFilter.MSOrder))
                         {
                             // Check if the scan has a centroid stream
                             if (scan.HasCentroidStream)

Writer/MzMlSpectrumWriter.cs

@@ -285,7 +285,7 @@ public override void Write(IRawDataPlus rawFile, int firstScanNumber, int lastSc
                     value = ""
                 });
                 _writer.WriteEndElement(); // processingMethod  
-                if (!ParseInput.NoPeakPicking)
+                if (ParseInput.NoPeakPicking.Count < ParseInput.AllLevels.Count)
                 {
                     _writer.WriteStartElement("processingMethod");
                     _writer.WriteAttributeString("order", "1");
@@ -1386,7 +1386,7 @@ private SpectrumType ConstructMSSpectrum(int scanNumber)
             double[] masses;
             double[] intensities;
 
-            if (!ParseInput.NoPeakPicking)
+            if (!ParseInput.NoPeakPicking.Contains((int)scanFilter.MSOrder))
             {
                 //Spectrum will be centroided
                 spectrumCvParams.Add(new CVParamType